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Find video protocols related to scientific articles indexed in Pubmed.
Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library.
Development
PUBLISHED: 10-09-2014
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Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures.
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Humoral response to calicivirus in captive tigers given a dual-strain vaccine.
J. Zoo Wildl. Med.
PUBLISHED: 04-10-2014
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The current feline vaccine with a single strain of calicivirus has been used for captive tigers, yet it may not protect against virulent systemic calicivirus infections. A cross-institutional study investigated the humoral response to a new dual-strain, killed-virus calicivirus vaccine for nine captive tigers. The subspecies of these tigers were Amur (Panthera tigris altaica), Bengal (Panthera tigris tigris), and Malayan (Panthera tigris jacksoni). Serum neutralization titers for virulent feline calicivirus strain FCV-DD1 were higher following dual-strain vaccine administration. There were no reports of adverse vaccine reactions. Dual-strain vaccination may afford broadened cross-protection against different calicivirus strains and is desirable to reduce the risk of virulent systemic calicivirus disease in tigers.
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A systematic nomenclature for the insect brain.
Neuron
PUBLISHED: 02-25-2014
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Despite the importance of the insect nervous system for functional and developmental neuroscience, descriptions of insect brains have suffered from a lack of uniform nomenclature. Ambiguous definitions of brain regions and fiber bundles have contributed to the variation of names used to describe the same structure. The lack of clearly determined neuropil boundaries has made it difficult to document precise locations of neuronal projections for connectomics study. To address such issues, a consortium of neurobiologists studying arthropod brains, the Insect Brain Name Working Group, has established the present hierarchical nomenclature system, using the brain of Drosophila melanogaster as the reference framework, while taking the brains of other taxa into careful consideration for maximum consistency and expandability. The following summarizes the consortium's nomenclature system and highlights examples of existing ambiguities and remedies for them. This nomenclature is intended to serve as a standard of reference for the study of the brain of Drosophila and other insects.
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NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo.
Front Cell Neurosci
PUBLISHED: 01-13-2014
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microRNAs (miRNAs) are major regulators of protein synthesis in the brain. A major goal is to identify changes in miRNA expression underlying protein synthesis-dependent forms of synaptic plasticity such as long-term potentiation (LTP). Previous analyses focused on changes in miRNA levels in total lysate samples. Here, we asked whether changes in total miRNA accurately reflect changes in the amount of miRNA bound to Argonaute protein within the miRNA-induced silencing complex (miRISC). Ago2 immunoprecipitation was used to isolate RISC-associated miRNAs following high-frequency stimulation (HFS)-induced LTP in the dentate gyrus of anesthetized rats. Using locked-nucleic acid-based PCR cards for high-throughput screening and independent validation by quantitative TaqMan RT-PCR, we identified differential regulation of Ago2-associated and total miRNA expression. The ratio of Ago2/total miRNA expression was regulated bidirectionally in a miRNA-specific manner and was largely dependent on N-methyl-D-aspartate receptor (NMDA) activation during LTP induction. The present results identify miRNA association with Ago2 as a potential control point in activity-dependent synaptic plasticity in the adult brain. Finally, novel computational analysis for targets of the Ago2-associated miRNAs identifies 21 pathways that are enriched and differentially targeted by the miRNAs including axon guidance, mTOR, MAPK, Ras, and LTP.
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A simulator for spatially extended kappa models.
Bioinformatics
PUBLISHED: 09-09-2013
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Spatial Kappa is a simulator of models written in a variant of the rule-based stochastic modelling language Kappa, with spatial extensions.
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An anatomic study of the distal femoral epiphysis.
J Pediatr Orthop
PUBLISHED: 07-02-2013
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The anatomy of the undulating distal femoral physis may be relevant to growth disturbance after physeal fractures and screw fixation about the physis. The surface anatomy of this physis has not been well described.
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An anatomic study of the epiphyseal tubercle and its importance in the pathogenesis of slipped capital femoral epiphysis.
J Bone Joint Surg Am
PUBLISHED: 03-22-2013
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It has been proposed that the epiphyseal tubercle on the inferior surface of the capital femoral epiphysis may be responsible for the clinical distinction between a stable and an unstable slipped capital femoral epiphysis (SCFE). The anatomy of the tubercle and its relationship to the lateral epiphyseal vessels have not previously been rigorously defined.
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Discrimination of individual tigers (Panthera tigris) from long distance roars.
J. Acoust. Soc. Am.
PUBLISHED: 03-08-2013
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This paper investigates the extent of tiger (Panthera tigris) vocal individuality through both qualitative and quantitative approaches using long distance roars from six individual tigers at Omahas Henry Doorly Zoo in Omaha, NE. The framework for comparison across individuals includes statistical and discriminant function analysis across whole vocalization measures and statistical pattern classification using a hidden Markov model (HMM) with frame-based spectral features comprised of Greenwood frequency cepstral coefficients. Individual discrimination accuracy is evaluated as a function of spectral model complexity, represented by the number of mixtures in the underlying Gaussian mixture model (GMM), and temporal model complexity, represented by the number of sequential states in the HMM. Results indicate that the temporal pattern of the vocalization is the most significant factor in accurate discrimination. Overall baseline discrimination accuracy for this data set is about 70% using high level features without complex spectral or temporal models. Accuracy increases to about 80% when more complex spectral models (multiple mixture GMMs) are incorporated, and increases to a final accuracy of 90% when more detailed temporal models (10-state HMMs) are used. Classification accuracy is stable across a relatively wide range of configurations in terms of spectral and temporal model resolution.
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Metabolic turnover of synaptic proteins: kinetics, interdependencies and implications for synaptic maintenance.
PLoS ONE
PUBLISHED: 01-01-2013
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Chemical synapses contain multitudes of proteins, which in common with all proteins, have finite lifetimes and therefore need to be continuously replaced. Given the huge numbers of synaptic connections typical neurons form, the demand to maintain the protein contents of these connections might be expected to place considerable metabolic demands on each neuron. Moreover, synaptic proteostasis might differ according to distance from global protein synthesis sites, the availability of distributed protein synthesis facilities, trafficking rates and synaptic protein dynamics. To date, the turnover kinetics of synaptic proteins have not been studied or analyzed systematically, and thus metabolic demands or the aforementioned relationships remain largely unknown. In the current study we used dynamic Stable Isotope Labeling with Amino acids in Cell culture (SILAC), mass spectrometry (MS), Fluorescent Non-Canonical Amino acid Tagging (FUNCAT), quantitative immunohistochemistry and bioinformatics to systematically measure the metabolic half-lives of hundreds of synaptic proteins, examine how these depend on their pre/postsynaptic affiliation or their association with particular molecular complexes, and assess the metabolic load of synaptic proteostasis. We found that nearly all synaptic proteins identified here exhibited half-lifetimes in the range of 2-5 days. Unexpectedly, metabolic turnover rates were not significantly different for presynaptic and postsynaptic proteins, or for proteins for which mRNAs are consistently found in dendrites. Some functionally or structurally related proteins exhibited very similar turnover rates, indicating that their biogenesis and degradation might be coupled, a possibility further supported by bioinformatics-based analyses. The relatively low turnover rates measured here (?0.7% of synaptic protein content per hour) are in good agreement with imaging-based studies of synaptic protein trafficking, yet indicate that the metabolic load synaptic protein turnover places on individual neurons is very substantial.
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The Virtual Fly Brain browser and query interface.
Bioinformatics
PUBLISHED: 12-16-2011
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Sources of neuroscience data in Drosophila are diverse and disparate making integrated search and retrieval difficult. A major obstacle to this is the lack of a comprehensive and logically structured anatomical framework and an intuitive interface.
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Towards a quantitative model of the post-synaptic proteome.
Mol Biosyst
PUBLISHED: 08-26-2011
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The postsynaptic compartment of the excitatory glutamatergic synapse contains hundreds of distinct polypeptides with a wide range of functions (signalling, trafficking, cell-adhesion, etc.). Structural dynamics in the post-synaptic density (PSD) are believed to underpin cognitive processes. Although functionally and morphologically diverse, PSD proteins are generally enriched with specific domains, which precisely define the mode of clustering essential for signal processing. We applied a stochastic calculus of domain binding provided by a rule-based modelling approach to formalise the highly combinatorial signalling pathway in the PSD and perform the numerical analysis of the relative distribution of protein complexes and their sizes. We specified the combinatorics of protein interactions in the PSD by rules, taking into account protein domain structure, specific domain affinity and relative protein availability. With this model we interrogated the critical conditions for the protein aggregation into large complexes and distribution of both size and composition. The presented approach extends existing qualitative protein-protein interaction maps by considering the quantitative information for stoichiometry and binding properties for the elements of the network. This results in a more realistic view of the postsynaptic proteome at the molecular level.
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Comparison of carfentanil-xylazine and thiafentanil-medetomidine in electroejaculation of captive gaur (Bos gaurus).
J. Zoo Wildl. Med.
PUBLISHED: 07-28-2011
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Carfentanil citrate and thiafentanil oxalate have been used successfully to immobilize captive and free-ranging ungulates. The objective of this study was to compare the efficacy and certain physiologic parameters of protocols by using the 2 opioids in gaur (Bos gaurus). Eight adult gaur bulls were immobilized for electroejaculation at Omahas Henry Doorly Zoo (Omaha, Nebraska, USA). All the animals were immobilized twice, by using each of the following protocols one time: 10 mg carfentanil combined with 100 mg xylazine (CX), reversed with 1,000 mg naltrexone and 24 mg yohimbine; and 12 mg thiafentanil combined with 20 mg medetomidine (TM), reversed with 120 mg naltrexone and 100 mg atipamezole. Immobilization drugs were delivered intramuscularly into the shoulder area via pole syringe. Electroejaculation was carried out by a standardized protocol to duplicate procedural stimulation on each animal. Induction and recovery times, initial rectal temperature, heart rate, respiratory rate, anesthetic depth, oxygen saturation, indirect blood pressure, and arterial blood gases were recorded at the time of initial handling, before ejaculation, and after ejaculation. Antagonists were administered 1/4 i.v. and 3/4 s.q. Both protocols require a small volume of drug for a large ungulate, provide smooth induction, and adequate anesthesia. Both protocols produced a significant hypoxemia, although the animals on CX showed slightly better blood gas values (based on lower partial pressure of carbon dioxide) and numerically lower blood pressure values. Animals on TM had better muscle relaxation and smoother recoveries, with no renarcotization noted. The results of the present study indicate the TM and CX protocols used for immobilizing gaur result in similar quality ejaculates that can be used for fertility examination as well as for assisted reproduction such as artificial insemination. Additional immobilizations need to take place to further compare these 2 combinations in this species.
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Biologically inspired EM image alignment and neural reconstruction.
Bioinformatics
PUBLISHED: 07-08-2011
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Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden.
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Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes.
Bioinformatics
PUBLISHED: 07-04-2011
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Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.
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Clinical and pathologic characteristics of T-cell lymphoma with a leukemic phase in a raccoon dog (Nyctereutes procyonoides).
J. Vet. Diagn. Invest.
PUBLISHED: 06-07-2011
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A 7.5-year-old raccoon dog (Nyctereutes procyonoides) from the Henry Doorly Zoo (Omaha, Nebraska) presented to the veterinary hospital for lethargy and weight loss. On physical examination, splenomegaly and hepatomegaly were noted on palpation and were confirmed by radiographic evaluation. Radiography also demonstrated a mass in the cranial mediastinum. A complete blood cell count revealed marked leukocytosis (115,200 cells/µl), with a predominance of lymphoid cells. The animal was euthanized due to a poor prognosis. Necropsy revealed splenomegaly, hepatomegaly, and a large multiloculated mass in the cranial mediastinum. The histologic and immunohistochemical diagnosis was multicentric T-cell lymphoma with a leukemic phase.
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Dietary salt levels affect salt preference and learning in larval Drosophila.
PLoS ONE
PUBLISHED: 04-25-2011
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Drosophila larvae change from exhibiting attraction to aversion as the concentration of salt in a substrate is increased. However, some aversive concentrations appear to act as positive reinforcers, increasing attraction to an odour with which they have been paired. We test whether this surprising dissociation between the unconditioned and conditioned response depends on the larvaes experience of salt concentration in their food. We find that although the point at which a NaCl concentration becomes aversive shifts with different rearing experience, the dissociation remains evident. Testing larvae using a substrate 0.025 M above the NaCl concentration on which the larvae were reared consistently results in aversive choice behaviour but appetitive reinforcement effects.
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Double rib penetration of the spinal canal in a patient with neurofibromatosis.
J Pediatr Orthop
PUBLISHED: 04-13-2011
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Rib head penetration into the spinal canal in patients with severe kyphoscoliosis secondary to neurofibromatosis type-1 (NF-1) is extremely rare. Double rib head penetration has only been reported once earlier.
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Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder.
PLoS ONE
PUBLISHED: 03-21-2011
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Current models of schizophrenia and bipolar disorder implicate multiple genes, however their biological relationships remain elusive. To test the genetic role of glutamate receptors and their interacting scaffold proteins, the exons of ten glutamatergic hub genes in 1304 individuals were re-sequenced in case and control samples. No significant difference in the overall number of non-synonymous single nucleotide polymorphisms (nsSNPs) was observed between cases and controls. However, cluster analysis of nsSNPs identified two exons encoding the cysteine-rich domain and first transmembrane helix of GRM1 as a risk locus with five mutations highly enriched within these domains. A new splice variant lacking the transmembrane GPCR domain of GRM1 was discovered in the human brain and the GRM1 mutation cluster could perturb the regulation of this variant. The predicted effect on individuals harbouring multiple mutations distributed in their ten hub genes was also examined. Diseased individuals possessed an increased load of deleteriousness from multiple concurrent rare and common coding variants. Together, these data suggest a disease model in which the interplay of compound genetic coding variants, distributed among glutamate receptors and their interacting proteins, contribute to the pathogenesis of schizophrenia and bipolar disorders.
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The current medical practice of the pediatric orthopaedic surgeon in North America.
J Pediatr Orthop
PUBLISHED: 03-19-2011
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Musculoskeletal disorders in children are common and comprise 20% to 30% of the complaints observed by primary care physicians. Most primary care physicians prefer to refer patients with pediatric musculoskeletal conditions to the pediatric orthopaedic surgeon; most of whom are treated nonoperatively. Pediatric orthopaedic surgeons are well trained to provide efficient, cost-effective, and definitive quality care. This article supports the supposition that pediatric orthopaedic surgeons are the primary care physicians for children with musculoskeletal disorders. This article focuses on the primary clinical responsibilities of the pediatric orthopaedic surgeon, describes the value of this practice, and contrasts their responsibilities from that of other orthopaedic subspecialties.
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A model of non-elemental olfactory learning in Drosophila.
J Comput Neurosci
PUBLISHED: 03-07-2011
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The pathways for olfactory learning in the fruitfly Drosophila have been extensively investigated, with mounting evidence that that the mushroom body is the site of the olfactory associative memory trace (Heisenberg, Nature 4:266-275, 2003; Gerber et al., Curr Opin Neurobiol 14:737-744, 2004). Heisenbergs description of the mushroom body as an associative learning device is a testable hypothesis that relates the mushroom bodys function to its neural structure and input and output pathways. Here, we formalise a relatively complete computational model of the network interactions in the neural circuitry of the insect antennal lobe and mushroom body, to investigate their role in olfactory learning, and specifically, how this might support learning of complex (non-elemental; Giurfa, Curr Opin Neuroethol 13:726-735, 2003) discriminations involving compound stimuli. We find that the circuit is able to learn all tested non-elemental paradigms. This does not crucially depend on the number of Kenyon cells but rather on the connection strength of projection neurons to Kenyon cells, such that the Kenyon cells require a certain number of coincident inputs to fire. As a consequence, the encoding in the mushroom body resembles a unique cue or configural representation of compound stimuli (Pearce, Psychol Rev 101:587-607, 1994). Learning of some conditions, particularly negative patterning, is strongly affected by the assumption of normalisation effects occurring at the level of the antennal lobe. Surprisingly, the learning capacity of this circuit, which is a simplification of the actual circuitry in the fly, seems to be greater than the capacity expressed by the fly in shock-odour association experiments (Young et al. 2010).
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Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.
BMC Bioinformatics
PUBLISHED: 02-25-2011
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Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or interologs. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for on-the-fly interolog prediction.
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The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons.
PLoS Biol.
PUBLISHED: 01-04-2011
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In neurogenesis, neural cell fate specification is generally triggered by proneural transcription factors. Whilst the role of proneural factors in fate specification is well studied, the link between neural specification and the cellular pathways that ultimately must be activated to construct specialised neurons is usually obscure. High-resolution temporal profiling of gene expression reveals the events downstream of atonal proneural gene function during the development of Drosophila chordotonal (mechanosensory) neurons. Among other findings, this reveals the onset of expression of genes required for construction of the ciliary dendrite, a key specialisation of mechanosensory neurons. We determine that atonal activates this cellular differentiation pathway in several ways. Firstly, atonal directly regulates Rfx, a well-known highly conserved ciliogenesis transcriptional regulator. Unexpectedly, differences in Rfx regulation by proneural factors may underlie variations in ciliary dendrite specialisation in different sensory neuronal lineages. In contrast, fd3F encodes a novel forkhead family transcription factor that is exclusively expressed in differentiating chordotonal neurons. fd3F regulates genes required for specialized aspects of chordotonal dendrite physiology. In addition to these intermediate transcriptional regulators, we show that atonal directly regulates a novel gene, dilatory, that is directly associated with ciliogenesis during neuronal differentiation. Our analysis demonstrates how early cell fate specification factors can regulate structural and physiological differentiation of neuronal cell types. It also suggests a model for how subtype differentiation in different neuronal lineages may be regulated by different proneural factors. In addition, it provides a paradigm for how transcriptional regulation may modulate the ciliogenesis pathway to give rise to structurally and functionally specialised ciliary dendrites.
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Mixed infection with reovirus and Chlamydophila in a flock of budgerigars (Melopsittacus undulatus).
J. Avian Med. Surg.
PUBLISHED: 12-28-2010
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Eleven budgerigars (Melopsittacus undulatus) from a zoological collection presented at necropsy with emaciation and splenomegaly or hepatomegaly or both. Polymerase chain reaction assays performed on liver and spleen samples were positive for Chlamydophila psittaci in 2 of 3 birds tested, and histologic findings in 2 additional birds were compatible with chlamydiosis. The aviary was subsequently closed to the public, and a 45-day treatment regimen with doxycycline in the seeds was initiated. No further deaths of birds with hepatomegaly or splenomegaly were observed after the first day of treatment. Further investigation of birds that died during the outbreak with emaciation and with hepatic and splenic enlargement revealed severe necrosis of the spleen and liver suggestive of reovirus infection, which was supported with polymerase chain reaction analysis from paraffin-embedded tissue. This reovirus was sequenced and had 100% homology with a reovirus previously identified in an African grey parrot (Psittacus erithacus). The outbreak did not affect cockatiels (Nymphicus hollandicus) and blue quail (Coturnix chinensis) kept in the same aviary. A group of budgerigars added to the collection soon before the opening of the aviary may have introduced reovirus and Chlamydophila into the collection.
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Vocal power and pressure-flow relationships in excised tiger larynges.
J. Exp. Biol.
PUBLISHED: 11-02-2010
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Despite the functional importance of loud, low-pitched vocalizations in big cats of the genus Panthera, little is known about the physics and physiology of the mechanisms producing such calls. We investigated laryngeal sound production in the laboratory using an excised-larynx setup combined with sound-level measurements and pressure-flow instrumentation. The larynges of five tigers (three Siberian or Amur, one generic non-pedigreed tiger with Bengal ancestry and one Sumatran), which had died of natural causes, were provided by Omahas Henry Doorly Zoo over a five-year period. Anatomical investigation indicated the presence of both a rigid cartilaginous plate in the arytenoid portion of the glottis, and a vocal fold fused with a ventricular fold. Both of these features have been confusingly termed vocal pads in the previous literature. We successfully induced phonation in all of these larynges. Our results showed that aerodynamic power in the glottis was of the order of 1.0 W for all specimens, acoustic power radiated (without a vocal tract) was of the order of 0.1 mW, and fundamental frequency ranged between 20 and 100 Hz when a lung pressure in the range of 0-2.0 kPa was applied. The mean glottal airflow increased to the order of 1.0 l s(-1) per 1.0 kPa of pressure, which is predictable from scaling human and canine larynges by glottal length and vibrational amplitude. Phonation threshold pressure was remarkably low, on the order of 0.3 kPa, which is lower than for human and canine larynges phonated without a vocal tract. Our results indicate that a vocal fold length approximately three times greater than that of humans is predictive of the low fundamental frequency, and the extraordinarily flat and broad medial surface of the vocal folds is predictive of the low phonation threshold pressure.
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Morbillivirus infection in a wild siberian tiger in the Russian Far East.
J. Wildl. Dis.
PUBLISHED: 10-23-2010
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We report the first documented case of morbillivirus infection in a wild, free-ranging Siberian tiger (Panthera tigris altaica). The tigress entered a small village in the Russian Far East in an ambulatory but stuporous state with no apparent recognition or fear of humans. Her condition progressed rapidly with neurological signs, anorexia, and ultimately death. Histologic lesions included vacuolated to malacic white matter in the brain stem, cerebellum, and thalamus, with associated lymphocytic meningoencephalitis. Large, intranuclear, eosinophilic inclusions were within regional astrocytes, and the brain lesions were immunohistochemically positive when stained for canine distemper viral antigen. Hematologic and blood chemistry results were consistent with overwhelming systemic infection and starvation. The animal also was antibody-positive for canine distemper virus, feline panleukopenia, and feline coronavirus.
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Dermatitis in captive Wyoming toads (Bufo baxteri) associated with Fusarium spp.
J. Wildl. Dis.
PUBLISHED: 10-23-2010
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From May 2007 to June 2008, 30 of 49 Wyoming toads (Bufo baxteri) kept at Omahas Henry Doorly Zoo (Nebraska, USA) died showing clinical signs of ventral erythema, inappetance, lethargy, and delayed righting reflex. Treatment with antifungals and antibiotics was unsuccessful in all cases. Histopathologic analyses revealed dermatitis as the primary problem in 20 of 21 toads in which skin was examined. Fungal dermatitis was present in 17 toads, with hyphae approximately 1-3 ?m in diameter, and parallel cell walls and frequent septations. In 14 animals, the fungal dermatitis was the main pathologic lesion. Several species of bacteria were associated with all cases. A few animals tested positive for Ranavirus using polymerase chain reaction. Fusarium sp. was consistently cultured from skin, feces, kidneys, and from powdered food provided to crickets. Four isolates were identified as Fusarium proliferatum, Fusarium oxysporum, Fusarium solani, and Fusarium verticillioides, which suggested a secondary role of fungi. A specific underlying cause of disease could not be found, although the roles of humidity and Ranavirus infection are discussed, along with the well-known susceptibility of bufonids to fungal dermatitis.
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Merged consensus clustering to assess and improve class discovery with microarray data.
BMC Bioinformatics
PUBLISHED: 08-24-2010
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One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups. There are a large number of methods available to perform clustering, but it is often unclear which method is best suited to the data and how to quantify the quality of the classifications produced.
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Scoliosis in a tiger salamander (Ambystoma tigrinum) associated with encysted digenetic trematodes of the genus Clinostomum.
J. Wildl. Dis.
PUBLISHED: 08-07-2010
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A group of 202 tiger salamanders (Ambystoma tigrinum) was brought into captivity due to habitat destruction. Half of these animals died, over two mo, showing generalized hemorrhages compatible with an infectious disease, but an etiologic agent was not determined. Encysted metacercarial stages of trematodes within the skeletal musculature, coelomic cavity, and subcutaneous space were additional necropsy findings. One salamander had scoliosis and multiple skin nodules. A radiograph showed no skeletal abnormality to explain the scoliosis; however, numerous round nodules were more radiodense than the surrounding tissue. A presumptive diagnosis of generalized trematodiasis was made, yet the salamander did not improve after a course of praziquantel and subsequently died. Necropsy revealed massive, encysted trematode infection. Histologic examination revealed marked multifocal intramuscular, subcutaneous, and coelomic trematodiasis with associated necrosis and inflammation. Based on gross morphology, the trematode was identified as a member of the genus Clinostomum.
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BrainTrap: a database of 3D protein expression patterns in the Drosophila brain.
Database (Oxford)
PUBLISHED: 07-14-2010
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Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D-expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at http://fruitfly.inf.ed.ac.uk/braintrap, an online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila. Full size images throughout the volume of the entire brain can be viewed interactively in a web browser. The database includes searchable annotations linked to the FlyBase Drosophila anatomy ontology. Anatomical search criteria can be specified using automatic completion and a hierarchical browser for the ontology. The provenance of all annotation is retained and the location where the annotator made the conclusion can be highlighted. Database URL: http://fruitfly.inf.ed.ac.uk/braintrap.
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Circadian control of mouse heart rate and blood pressure by the suprachiasmatic nuclei: behavioral effects are more significant than direct outputs.
PLoS ONE
PUBLISHED: 02-25-2010
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Diurnal variations in the incidence of events such as heart attack and stroke suggest a role for circadian rhythms in the etiology of cardiovascular disease. The aim of this study was to assess the influence of the suprachiasmatic nucleus (SCN) circadian clock on cardiovascular function.
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Comparison of supine bending, push-prone, and traction under general anesthesia radiographs in predicting curve flexibility and postoperative correction in adolescent idiopathic scoliosis.
Spine
PUBLISHED: 01-30-2010
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A prospective study comparing supine bending, push-prone, and traction under general anesthesia (UGA) radiographs in adolescent idiopathic scoliosis.
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Herpesvirus infections in rock hyraxes (Procavia capensis).
J. Vet. Diagn. Invest.
PUBLISHED: 07-01-2009
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Seven juveniles and 3 adults from a closed group of 19 rock hyraxes (Procavia capensis) housed in a zoos indoor rock exhibit died or were euthanized after developing blepharoconjunctivitis and orofacial ulcers over a 2-week period. Histopathologic examination of dermal ulcers and ulcerated tongues revealed amphophilic to basophilic intranuclear inclusion bodies in epithelial cells bordering ulcers. Epithelial cells with inclusion bodies were often characterized by cytomegaly and karyomegaly, and many cells had formed syncytia. Examination of inclusion bodies in tongue epithelium by transmission electron microscopy revealed icosahedral nucleocapsids, approximately 80-95 nm in diameter, with morphologic features consistent with herpesvirus. Cytopathic effect (CPE) typical of alphaherpesvirus infection was seen in bovine turbinate, equine dermal, and Vero cell monolayers after inoculation with homogenates of the skin lesions, but CPE was not seen after inoculation onto Madin-Darby canine kidney or swine testicle cell monolayers. Polymerase chain reaction analysis using degenerate primers that targeted a portion of the herpesvirus polymerase gene generated a product of approximately 227 base pairs. The product was cloned, sequenced, and then analyzed using BLAST. At the nucleotide level, there was 86%, 77%, and 76% shared identity with Eidolon herpesvirus 1, Human herpesviruses 1 and 2, and Cercopithecine herpesvirus 2, respectively. Herpesvirus infections in rock hyraxes have not been characterized. The data presented in the current study suggest that a novel alphaherpesvirus caused the lesions seen in these rock hyraxes. The molecular characteristics of this virus would tentatively support its inclusion in the genus Simplexvirus.
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Towards a virtual fly brain.
Philos Trans A Math Phys Eng Sci
PUBLISHED: 05-06-2009
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Models of the brain that simulate sensory input, behavioural output and information processing in a biologically plausible manner pose significant challenges to both computer science and biology. Here we investigated strategies that could be used to create a model of the insect brain, specifically that of Drosophila melanogaster that is very widely used in laboratory research. The scale of the problem is an order of magnitude above the most complex of the current simulation projects, and it is further constrained by the relative sparsity of available electrophysiological recordings from the fly nervous system. However, fly brain research at the anatomical and behavioural levels offers some interesting opportunities that could be exploited to create a functional simulation. We propose to exploit these strengths of Drosophila central nervous system research to focus on a functional model that maps biologically plausible network architecture onto phenotypic data from neuronal inhibition and stimulation studies, leaving aside biophysical modelling of individual neuronal activity for future models until more data are available.
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A neural circuit mechanism integrating motivational state with memory expression in Drosophila.
Cell
PUBLISHED: 04-01-2009
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Behavioral expression of food-associated memory in fruit flies is constrained by satiety and promoted by hunger, suggesting an influence of motivational state. Here, we identify a neural mechanism that integrates the internal state of hunger and appetitive memory. We show that stimulation of neurons that express neuropeptide F (dNPF), an ortholog of mammalian NPY, mimics food deprivation and promotes memory performance in satiated flies. Robust appetitive memory performance requires the dNPF receptor in six dopaminergic neurons that innervate a distinct region of the mushroom bodies. Blocking these dopaminergic neurons releases memory performance in satiated flies, whereas stimulation suppresses memory performance in hungry flies. Therefore, dNPF and dopamine provide a motivational switch in the mushroom body that controls the output of appetitive memory.
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Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.
Mol. Syst. Biol.
PUBLISHED: 04-01-2009
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The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K+ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage-dependent K+ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.
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G2Cdb: the Genes to Cognition database.
Nucleic Acids Res.
PUBLISHED: 03-04-2009
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Neuroscience databases linking genes, proteins, (patho)physiology, anatomy and behaviour across species will be valuable in a broad range of studies of the nervous system. G2Cdb is such a neuroscience database aiming to present a global view of the role of synapse proteins in physiology and disease. G2Cdb warehouses sets of genes and proteins experimentally elucidated by proteomic mass spectroscopy of signalling complexes and proteins biochemically isolated from mammalian synapse preparations, giving an experimentally validated definition of the constituents of the mammalian synapse. Using automated text-mining and expert (human) curation we have systematically extracted information from published neurobiological studies in the fields of synaptic signalling electrophysiology and behaviour in knockout and other transgenic mice. We have also surveyed the human genetics literature for associations to disease caused by mutations in synaptic genes. The synapse proteome datasets that G2Cdb provides offer a basis for future work in synapse biology and provide useful information on brain diseases. They have been integrated in a such way that investigators can rapidly query whether a gene or protein is found in brain-signalling complex(es), has a phenotype in rodent models or whether mutations are associated with a human disease. G2Cdb can be freely accessed at http://www.genes2cognition.org.
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Safety and immunogenicity of the Mycobacterium tuberculosis DeltalysA DeltapanCD vaccine in domestic cats infected with feline immunodeficiency virus.
Clin. Vaccine Immunol.
PUBLISHED: 01-14-2009
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Feline immunodeficiency virus (FIV)-positive and FIV-negative cats (n=4/group) received 2 x 10(6) CFU Mycobacterium tuberculosis DeltalysA DeltapanCD intramuscularly. Vaccination elicited antibody responses, albeit at lower levels in FIV-positive cats than in FIV-negative cats. Delayed-type hypersensitivity responses were minimal in both groups. No adverse reactions were found.
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An outbreak of avian mycobacteriosis caused by Mycobacterium intracellulare in little blue penguins (Eudyptula minor).
J. Zoo Wildl. Med.
PUBLISHED: 01-07-2009
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Mycobacterium intracellulare (MIT) was diagnosed postmortem by culture and supporting histopathology in seven birds from a flock of little blue penguins (Eudyptula minor) at the Henry Doorly Zoo (HDZ). These birds represented 20% of the deaths in the population over a 4 yr period. Clinical signs in affected birds included severe respiratory distress characterized by open-mouth breathing with chronic debilitation. On exam, plaques were noted in the larynx, trachea, and soft tissue of the caudal oropharynx. Index cases were identified on necropsy in two birds on loan to another institution in 2003. Following a case confirmed antemortem at the HDZ, a three-drug protocol of rifampin (15 mg/kg p.o. s.i.d.), ethambutol (15 mg/kg p.o. s.i.d.), and clarithromycin (10 mg/kg p.o. s.i.d.) was started on this bird in 2004 and extended to the entire flock in 2005. Gastric wash, fecal samples, and throat plaques were obtained antemortem on five birds within the flock, selected because of the presence of oral plaques, and tested by culture followed by a polymerase chain reaction assay. MIT was detected in gastric washes from four birds and in throat plaques from all five. Three more birds died during treatment. After the seventh bird died, antimicrobial susceptibility testing performed in July 2007 indicated that the MIT was now resistant to most antibiotics tested, including rifampin and ethambutol. The treatment regimen was changed to minocycline (10 mg/kg p.o. b.i.d.) and clarithromycin (10 mg/kg p.o. s.i.d.). Oral plaques were not seen on monthly rechecks of the flock through November 2008. The proposed mechanism of transmission is exposure to wild birds but the source has not been determined. These cases of avian mycobacteriosis caused by MIT are the first known cases reported in little blue penguins.
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Consolidation and translation regulation.
Learn. Mem.
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mRNA translation, or protein synthesis, is a major component of the transformation of the genetic code into any cellular activity. This complicated, multistep process is divided into three phases: initiation, elongation, and termination. Initiation is the step at which the ribosome is recruited to the mRNA, and is regarded as the major rate-limiting step in translation, while elongation consists of the elongation of the polypeptide chain; both steps are frequent targets for regulation, which is defined as a change in the rate of translation of an mRNA per unit time. In the normal brain, control of translation is a key mechanism for regulation of memory and synaptic plasticity consolidation, i.e., the off-line processing of acquired information. These regulation processes may differ between different brain structures or neuronal populations. Moreover, dysregulation of translation leads to pathological brain function such as memory impairment. Both normal and abnormal function of the translation machinery is believed to lead to translational up-regulation or down-regulation of a subset of mRNAs. However, the identification of these newly synthesized proteins and determination of the rates of protein synthesis or degradation taking place in different neuronal types and compartments at different time points in the brain demand new proteomic methods and system biology approaches. Here, we discuss in detail the relationship between translation regulation and memory or synaptic plasticity consolidation while focusing on a model of cortical-dependent taste learning task and hippocampal-dependent plasticity. In addition, we describe a novel systems biology perspective to better describe consolidation.
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A strategy for building neuroanatomy ontologies.
Bioinformatics
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Advancing our understanding of how nervous systems work will require the ability to store and annotate 3D anatomical datasets, recording morphology, partonomy and connectivity at multiple levels of granularity from subcellular to gross anatomy. It will also require the ability to integrate this data with other data-types including functional, genetic and electrophysiological data. The web ontology language OWL2 provides the means to solve many of these problems. Using it, one can rigorously define and relate classes of anatomical structure using multiple criteria. The resulting classes can be used to annotate datasets recording, for example, gene expression or electrophysiology. Reasoning software can be used to automate classification and error checking and to construct and answer sophisticated combinatorial queries. But for such queries to give consistent and biologically meaningful results, it is important that both classes and the terms (relations) used to relate them are carefully defined.
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Serosurvey of free-ranging Amur tigers in the Russian Far East.
J. Wildl. Dis.
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Wild Amur tigers (Panthera tigris altaica, n=44) from the Russian Far East were tested for antibodies to feline leukemia virus, feline corona virus (FCoV), feline immunodeficiency virus, feline parvovirus (FPV), canine distemper virus (CDV), Toxoplasma gondii, and Bartonella henselae. Antibodies to FCoV, CDV, FPV, and T. gondii were detected in 43, 15, 68, and 42% of tigers, respectively. No differences were detected in antibody prevalence estimates between tigers captured as part of a research program and those captured to mitigate human-tiger conflicts. Domestic dogs (Canis familiaris) were tested as a potential source for CDV; 16% were vaccinated against CDV and 58% of unvaccinated dogs were antibody positive for CDV. A high percentage of tigers were exposed to potential pathogens that could affect the survival of this species. We recommend continued monitoring of wild tigers throughout Asia, development of standardized sampling and postmortem examination procedures, and additional research to better understand potential domestic and wild animal sources for these pathogens.
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Transcriptional analysis of Gli3 mutants identifies Wnt target genes in the developing hippocampus.
Cereb. Cortex
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Early development of the hippocampus, which is essential for spatial memory and learning, is controlled by secreted signaling molecules of the Wnt gene family and by Wnt/?-catenin signaling. Despite its importance, little is known, however, about Wnt-regulated genes during hippocampal development. Here, we used the Gli3 mutant mouse extra-toes (Xt(J)), in which Wnt gene expression in the forebrain is severely affected, as a tool in a microarray analyses to identify potential Wnt target genes. This approach revealed 53 candidate genes with restricted or graded expression patterns in the dorsomedial telencephalon. We identified conserved Tcf/Lef-binding sites in telencephalon-specific enhancers of several of these genes, including Dmrt3, Gli3, Nfia, and Wnt8b. Binding of Lef1 to these sites was confirmed using electrophoretic mobility shift assays. Mutations in these Tcf/Lef-binding sites disrupted or reduced enhancer activity in vivo. Moreover, ectopic activation of Wnt/?-catenin signaling in an ex vivo explant system led to increased telencephalic expression of these genes. Finally, conditional inactivation of Gli3 results in defective hippocampal growth. Collectively, these data strongly suggest that we have identified a set of direct Wnt target genes in the developing hippocampus and provide inside into the genetic hierarchy underlying Wnt-regulated hippocampal development.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.