Monday Morning Eye Opener, May 16, 2016

Weekly Newsletter from the Northwest District Office for libraries containing programs, activities, classes for the upcoming week.

Monday Morning Eye Opener, May 23, 2016

Weekly Newsletter from the Northwest District Office for libraries containing programs, activities, classes for the upcoming week.

T cell recognition of hapten. Anatomy of T cell receptor binding of a H-2kd-associated photoreactive peptide derivative.

To elucidate the structural basis of T cell recognition of hapten-modified antigenic peptides, we studied the interaction of the T1 T cell antigen receptor (TCR) with its ligand, the H-2Kd-bound Plasmodium berghei circumsporozoite peptide 252-260 (SYIPSAEKI) containing photoreactive 4-azidobenzoic acid (ABA) on P. berghei circumsporozoite Lys259. The photoaffinity-labeled TCR residue(s) were mapped as Tyr48 and/or Tyr50 of complementary determining region 2beta (CDR2beta). Other TCR-ligand contacts were identified by mutational analysis. Molecular modeling, based on crystallographic coordinates of closely related TCR and major histocompatibility complex I molecules, indicated that ABA binds strongly and specifically in a cavity between CDR3alpha and CDR2beta. We conclude that TCR expressing selective Vbeta and CDR3alpha sequences form a binding domain between CDR3alpha and CDR2beta that can accommodate nonpeptidic moieties conjugated at the C-terminal portion of peptides binding to major histocompatibility complex (MHC) encoded proteins.

The 1925 Opium Purchasing Campaign in Laos: The Anatomy of a Colonial Scandal

Opium purchasing campaigns, initiated in 1915, were abruptly interrupted ten years later following the discovery that the Douanes & Régies of the General Government of Indochina had been victim of a gigantic fraud. Various inquiries expedited with a view to establishing responsibility for the fiasco, involving purchases made at Luang Prabang in 1925, highlight the dysfunctions affecting the colonial civil service. The 1925 scandal revealed not only the difficulties encountered by the French in their attempts to control the drug trade, but also the prevailing circumstantial inefficiency of the colonial bureaucracy.

Project SKY-EYE: applying UAVs to forest fire fighter support and monitoring

Peer reviewed

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/

Exploration of the visual system: Part 1: Dissection of the mouse eye for RNA, protein, and histological analyses

Due to the power of genetics, the mouse has become a widely used animal model in vision research. However, its eyeball has an axial length of only about 2 mm. The present protocol describes how to easily dissect the small rodent eye post mortem. This allows collecting different tissues of the eye, i.e., cornea, lens, iris, retina, optic nerve, retinal pigment epithelium (RPE), and sclera. We further describe in detail how to process these eye samples in order to obtain high‐quality RNA for RNA expression profiling studies. Depending on the eye tissue to be analyzed, we present appropriate lysis buffers to prepare total protein lysates for immunoblot and immuno‐precipitation analyses. Fixation, inclusion, embedding, and cryosectioning of the globe for routine histological analyses (HE staining, DAPI staining, immunohistochemistry, in situ hybridization) is further presented. These basic protocols should allow novice investigators to obtain eye tissue samples rapidly for their experiments.

An Image Enhancement Technique using MTF of Human eye

Image filtering is a highly demanded approach of image enhancement in digital imaging systems design. It is widely used in television and camera design technologies to improve the quality of an output image to avoid various problems such as image blurring problem thatgains importance in design of displays of large sizes and design of digital cameras. This thesis proposes a new image filtering method basedon visual characteristics of human eye such as MTF. In contrast to the traditional filtering methods based on human visual characteristics this thesis takes into account the anisotropy of the human eye vision. The proposed method is based on laboratory measurements of the human eye MTF and takes into account degradation of the image by the latter. This method improves an image in the way it will be degraded by human eye MTF to give perception of the original image quality. This thesis gives a basic understanding of an image filtering approach and the concept of MTF and describes an algorithm to perform an image enhancement based on MTF of human eye. Performed experiments have shown quite good results according to human evaluation. Suggestions to improve the algorithm are also given for the future improvements.

Evaluation of the integrity of human corneal epithelium maintained in organ-culture during eye banking using Corneamax®

Purpose: Mediums have been developed to conserve corneal endothelium in organ-culture during eye banking. CorneaMax® is used by 25% of Eye Bank in Europe. Only little is known about conservation of corneal epithelium with this medium during banking. Its preservation could be of interest in clinic to cure corneal disease with stem cells deficiency. Therefore, we wanted to examine the integrity of human corneal epithelium maintained in CorneaMax®. Methods: Human corneas, considered unsuitable for transplantation, were obtained from the Eye Bank in Lausanne. Average post-mortem time was 14 hours. Cornoscleral rings were maintained in organ-culture in Corneamax® at 32°C. Samples were formalin-fixed after period ranging from 0 (D0) to 35 days (D35, N=5 for each time points) and stained with H&E. Proliferation and apoptosis were evaluated by immunostaining with antibody against Ki67 and Caspase3 respectively. Results: Corneas, which were not in organ-cultured (D0), showed different morphology, including intact epithelium with 5 to 7 layers, but also completely denuded basement membrane. In two cases, at D0, the epithelium lost its adherence to the basal lamina of the cornea creating a large epithelial sheet. During the two first days, corneas and limbus area lost totally their epithelium, except for some remaining limbal basal cells. From day 2 to day 10, regeneration of the epithelium took place, starting from the limbal region in direction to the central cornea. From day 10 to day 35, corneal epithelium appeared as an atrophic epithelium, consisting of only two cell layers. Proliferation happened in the whole cornea during the 35 days of organ-culture, as shown by Ki67 positive cells. Apoptosis was rarely detected in the corneal epithelium. Conclusions: Corneas maintained in CorneaMax® showed a complete disappearance of the corneal epithelium during the two first days and a conservation of limbal basal cells in the limbal region. These remaining cells allowed a full regeneration of the tissue, leading to an atrophic epithelium, composed of only two cell layers. This atrophic epithelium could be seen in all the organ-cultured corneas during the 35 days of conservation. This study is a first step to develop medium in organ-culture in order to conserve corneal epithelial cells.

Evaluation of a novel biomaterial in the suprachoroidal space of the rabbit eye.

PURPOSE: Drug delivery to treat diseases of the posterior segment of the eye, such as choroidal neovascularization and its complications, is hampered by poor intraocular penetration and rapid elimination of the drug from the eye. The purpose of this study was to investigate the feasibility and tolerance of suprachoroidal injections of poly(ortho ester) (POE), a bioerodible and biocompatible polymer, as a biomaterial potentially useful for development of sustained drug delivery systems. METHODS: After tunnelization of the sclera, different formulations based on POE were injected (100 microL) into the suprachoroidal space of pigmented rabbits and compared with 1% sodium hyaluronate. Follow-up consisted of fundus observations, echography, fluorescein angiography, and histologic analysis over 3 weeks. RESULTS: After injection, POE spread in the suprachoroidal space at the posterior pole. It was well tolerated and progressively disappeared from the site of injection without sequelae. No bleeding or retinal detachment occurred. Echographic pictures showed that the material was present in the suprachoroidal space for 3 weeks. Angiography revealed minor pigment irregularities at the site of injection, but no retinal edema or necrosis. Histology showed that POE was well tolerated in the choroid. CONCLUSIONS: POE suprachoroidal injections, an easy, controllable, and reproducible procedure, were well tolerated in the rabbit eye. POE appears to be a promising biomaterial to deliver drugs focally to the choroid and the retina.

Percutaneous biopsy through the foramen ovale for parasellar lesions: surgical anatomy, method, and indications.

Knowledge of the pathological diagnosis before deciding the best strategy for treating parasellar lesions is of prime importance, due to the relative high morbidity and side-effects of open direct approaches to this region, known to be rich in important vasculo-nervous structures. When imaging is not evocative enough to ascertain an accurate pathological diagnosis, a percutaneous biopsy through the transjugal-transoval route (of Hartel) may be performed to guide the therapeutic decision.The chapter is based on the authors' experience in 50 patients who underwent the procedure over the ten past years. There was no mortality and only little (mostly transient) morbidity. Pathological diagnosis accuracy of the method revealed good, with a sensitivity of 0.83 and a specificity of 1.In the chapter the authors first recall the surgical anatomy background from personal laboratory dissections. They then describe the technical procedure, as well as the tissue harvesting method. Finally they define indications together with the decision-making process.Due to the constraint trajectory of the biopsy needle inserted through the Foramen Ovale, accessible lesions are only those located in the Meckel trigeminal Cave, the posterior sector of the cavernous sinus compartment, and the upper part of the petroclival region.The authors advise to perform this percutaneous biopsy method when imaging does not provide sufficient evidence of the pathological nature of the lesion, for therapeutic decision. Goal is to avoid unnecessary open surgery or radiosurgery, also inappropriate chemo-/radio-therapy.

Análisis de la arquitectura de webs mediante tests de estrés de navegación, de usabilidad y eye tracking

Evaluar una arquitectura de la información en un sitio web ya desplegado no resulta una tarea sencilla. La mayoría de las técnicas se centran en examinar la usabilidad del sistema que, aunque afecta a la arquitectura de la información, no es el único factor que influye en ella. La principal técnica que se utiliza es el test de estrés de navegación. Se muestra un aporte metodológico para hacer dicha técnica más informativa, llevándola más allá de la simple anotación en papel por parte del usuario de respuestas a las preguntas de navegación planteadas. Se propone la combinación de ésta con otras técnicas de evaluación de la usabilidad: la técnica de pensar en voz alta o thinking aloud y un cuestionario de usabilidad. Se ha utilizado un sistema de seguimiento de la mirada o eye tracking para complementar la información obtenida mediante las técnicas aplicadas. El enfoque metodológico planteado se ha puesto a prueba analizando una serie de sitios web de bibliotecas de universidades públicas españolas. Se muestra en los resultados la validez del enfoque empleado, así como el valor que dicho enfoque y el uso del eye tracking aportan al análisis de la arquitectura de la información respecto al test de estrés de navegación tradicional.

Short communication.Wood identification based on their common name and their transversal surface anatomy. Application to the batch from the expedition of Ruiz and Pavon

Aim of study: To identify species of wood samples based on common names and anatomical analyses of their transversal surfaces (without microscopic preparations). Area of study: Spain and South America Material and methods: The test was carried out on a batch of 15 lumber samples deposited in the Royal Botanical Garden in Madrid, from the expedition by Ruiz and Pavon (1777-1811). The first stage of the methodology is to search and to make a critical analysis of the databases which list common nomenclature along with scientific nomenclature. A geographic filter was then applied to the information resulting from the samples with a more restricted distribution. Finally an anatomical verification was carried out with a pocket microscope with a magnification of x40, equipped with a 50 micrometers resolution scale. Main results: The identification of the wood based exclusively on the common name is not useful due to the high number of alternative possibilities (14 for “naranjo”, 10 for “ébano”, etc.). The common name of one of the samples (“huachapelí mulato”) enabled the geographic origin of the samples to be accurately located to the shipyard area in Guayaquil (Ecuador). Given that Ruiz y Pavon did not travel to Ecuador, the specimens must have been obtained by Tafalla. It was possible to determine correctly 67% of the lumber samples from the batch. In 17% of the cases the methodology did not provide a reliable identification. Research highlights: It was possible to determine correctly 67% of the lumber samples from the batch and their geographic provenance. The identification of the wood based exclusively on the common name is not useful.