A study on formalizing the knowledge of data curation activities across different fields.

In recent years, with the trend of open science, there have been many efforts to share research data on the internet. To promote research data sharing, data curation is essential to make the data interpretable and reusable. In research fields such as life sciences, earth sciences, and social sciences, tasks and procedures have been already developed to implement efficient data curation to meet the needs and customs of individual research fields. However, not only data sharing within research fields but also interdisciplinary data sharing is required to promote open science. For this purpose, knowledge of data curation across the research fields is surveyed, analyzed, and organized as an ontology in this paper. As the survey, existing vocabularies and procedures are collected and compared as well as interviews with the data curators in research institutes in different fields are conducted to clarify commonalities and differences in data curation across the research fields. It turned out that the granularity of tasks and procedures that constitute the building blocks of data curation is not formalized. Without a method to overcome this gap, it will be challenging to promote interdisciplinary reuse of research data. Based on the analysis above, the ontology for the data curation process is proposed to describe data curation processes in different fields universally. It is described by OWL and shown as valid and consistent from the logical viewpoint. The ontology successfully represents data curation activities as the processes in the different fields acquired by the interviews. It is also helpful to identify the functions of the systems to support the data curation process. This study contributes to building a knowledge framework for an interdisciplinary understanding of data curation activities in different fields.

Concierge: personal database software for managing digital research resources.

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp).

Customizable neuroinformatics database system: XooNIps and its application to the pupil platform.

The developing field of neuroinformatics includes technologies for the collection and sharing of neuro-related digital resources. These resources will be of increasing value for understanding the brain. Developing a database system to integrate these disparate resources is necessary to make full use of these resources. This study proposes a base database system termed XooNIps that utilizes the content management system called XOOPS. XooNIps is designed for developing databases in different research fields through customization of the option menu. In a XooNIps-based database, digital resources are stored according to their respective categories, e.g., research articles, experimental data, mathematical models, stimulations, each associated with their related metadata. Several types of user authorization are supported for secure operations. In addition to the directory and keyword searches within a certain database, XooNIps searches simultaneously across other XooNIps-based databases on the Internet. Reviewing systems for user registration and for data submission are incorporated to impose quality control. Furthermore, XOOPS modules containing news, forums schedules, blogs and other information can be combined to enhance XooNIps functionality. These features provide better scalability, extensibility, and customizability to the general neuroinformatics community. The application of this system to data, models, and other information related to human pupils is described here.

Prostaglandins E1 and E2, but not F2alpha or latanoprost, inhibit monkey ciliary muscle contraction.

PURPOSE: To investigate the effects of prostaglandin (PG) E1, E2, F2alpha, and latanoprost acid on the electrically evoked contractile response of isolated rhesus monkey ciliary muscle. METHODS: Longitudinal ciliary muscle preparations from rhesus monkeys were mounted in an organ bath, and tension changes were recorded by an isometric transducer. Electrical field stimulation (100 Hz, 0.3 ms, 10 V) was applied through a pair of platinum plate electrodes. RESULTS: The ciliary muscle produced atropine-sensitive excitatory contraction in response to field stimulation. PGE1 and PGE2 (1 microM) attenuated the contraction to levels that were 68% and 65.1%, respectively, of the normal amplitude. However, PGF2alpha and latanoprost acid (1 microM) did not significantly change the response amplitude. CONCLUSIONS: Our results indicate that PGF2alpha and latanoprost acid do not interact with the prostanoid receptor involved at the pre- and/or postsynaptic site. Therefore, it is unlikely that the hypotensive action by these agents is due to relaxation of the ciliary muscle.

Action of biologically active peptides on monkey iris sphincter and dilator muscles.

Biologically active peptides modulate pupillary responsiveness in many non-primate mammals. We examined the action of seven different peptides on iris sphincter and dilator muscles of rhesus monkey. Iris sphincter and dilator muscle preparations from rhesus monkeys were mounted in an organ bath, and tension changes were recorded by an isometric transducer. Electrical field stimulation (100Hz, 0.3 msec, 10V) was applied through a pair of platinum plate electrodes. Monkey iris sphincter and dilator muscles produced simple cholinergic and adrenergic excitatory responses respectively to electrical field stimulation. Strong field stimulation did not elicit slow Substance P (SP) mediated contractions like those in rabbit iris sphincter. Exogenously applied pituitary adenylate cyclase-activating peptide (PACAP) enhanced in a concentration-dependent manner (0.3 nM-0.1 microm) the sphincter response to field stimulation, while neuropeptide Y (NPY) and somatostatin (SRIF) attenuated it. These three peptides did not affect sphincter contractions induced by acetylcholine, and therefore were acting at presynaptically. SP, calcitonin gene-related peptide (CGRP), vasoactive intestinal polypeptide (VIP) and galanin (GAL) had no effect (at 0.1 microm) on iris sphincter. None of seven exogenously applied peptides had an effect on monkey iris dilator muscle. The innervation of primate irises may be relatively simple compared to non-primates because each of the peptides in this study can modulate miosis or mydriasis in non-primate mammals. Future studies will be expected on the functional significance of species differences in iridial innervation.

Vasodilatory mechanism of unoprostone isopropyl on isolated rabbit ciliary artery.

PURPOSE: To clarify the vasodilatory mechanism of unoprostone isopropyl (unoprostone), a PG F2alpha related compound used for treatment of glaucoma, we have investigated the effect of this drug and its metabolites on isolated rabbit ciliary artery in vitro. METHODS: Under the dissecting microscope, ciliary arteries were prepared from albino rabbit eyes and mounted in a myograph system. The effects of unoprostone isopropyl and other agents were investigated using isometric tension recording methods. RESULTS: Unoprostone induced a dose-dependent relaxation in ciliary arteries that were pre-contracted with high-K solution, 10 microM histamine or 10 microM PG F2alpha. Neither unoprostone metabolite M1 or M2 had a relaxant effect on the precontracted vessels. Relaxation was unaffected by inhibition of adenylyl cyclase with SQ 22536, guanylyl cyclase with ODQ, or maxi-K channels with iberiotoxin. Pretreatment with unoprostone did not affect histamine-induced transient contractions in Ca2+ -free solution. However, SKF96365, a general Ca2+ channel blocker, evoked relaxation similar to unoprostone with respect to amplitude and rate of onset. CONCLUSIONS: Unoprostone, but not its metabolites M1 and M2, relaxed pre-contracted rabbit ciliary artery. The mechanism of vascular smooth muscle relaxation by unoprostone differs from that of IOP reduction and does not depend on adenylyl cyclase, guanylyl cyclase, or maxi-K channels. Relaxation may be mediated by inhibition of Ca2+ entry, possibly through capacitative Ca2+ channels.

Effect of somatostatin and galanin on isolated rabbit iris sphincter and dilator muscles.

The neuropeptides somatostatin and galanin are present in the iris and may modulate pupil diameter. We examined the effects of somatostatin and galanin on isolated rabbit iris dilator and sphincter smooth muscles that were mounted in an organ bath. An isometric transducer recorded changes in tension in response to electric field stimulation (100 Hz, 0.3 msec in duration, 10 V in strength) delivered by a pair of platinum plate electrodes. The dilator muscle response to field stimulation was not changed by either peptide, even at the highest concentrations examined. The sphincter muscle response consisted of two components: a fast component mediated by acetylcholine and slow component mediated by substance P. Both somatostatin and galanin attenuated the cholinergic component in a dose-dependent manner (from 0.3 nM to 0.1 microM) but had no effect on responses mediated by substance P. Galanin was more effective (attenuation of 43% at 0.1 microM) compared with somatostatin (attenuation of 16% at 0.1 microM) in reducing the cholinergic response. Neither peptide affected the contraction induced by acetylcholine (1mM). Therefore both peptides inhibited cholinergic transmission in the sphincter muscle, although the degree of inhibition by each was different. We conclude that somatostatin and/or galanin may induce mydriasis by attenuating cholinergic neurotransmitter release.

Mechanical properties of the rabbit iris smooth muscles.

The study focuses on obtaining the visco-elastic properties of the iris sphincter and dilator muscles. Two kinds of experiments were performed: the isometric contraction experiment and the isotonic quick release experiment. The length-tension relationship was obtained from the former experiment. This relationship clarified the contribution of each muscle in determining the statics of the pupil. The viscous and serial elastic properties were obtained from the latter experiment. The viscosity could be expressed by the expanded Hill's equation as a function of velocity and contractile tension. We argue that serial elasticity is independent of contractile tension. These properties provide insights into the pupillary mechanism.

Vasodilatory effects of nipradilol, an alpha- and beta-adrenergic blocker with nitric oxide releasing action, in rabbit ciliary artery.

Nipradilol is a new antiglaucoma ophthalmic agent used in Japan. Topical application of nipradilol is reported to increase ocular blood flow. To investigate the action of this drug, we studied the effect of nipradilol on the isolated rabbit ciliary artery. Under the dissecting microscope, ciliary arteries were prepared from rabbit eyes and mounted on a myograph system. The effects of nipradilol on the isolated rabbit ciliary artery were investigated using isometric tension recording methods. Nipradilol provoked a dose-dependent (10 microM-1m M) relaxation in ciliary arteries that were pre-contracted with high-K solutions (K(+): 100.7 m M). It also inhibited the amplitude of smooth muscle contraction evoked by field stimulation. Nipradilol was more effective in relaxing phenylephrine-induced contraction (EC(50): 21.6+/-16.3 microM) compared to high-K solution-induced contractions (EC(50): 230+/-130 microM). Application of N(w)-nitro- L -arginine methylester (300 microM), a nitric oxide (NO) synthase inhibitor, or denudations of endothelium by rubbing the inner surface with a scalp hair did not affect this relaxation. However, NO scavenger carboxy-PTIO (1m M) or methylene blue (10 microM), a guanylate cyclase inhibitor, inhibited the nipradilol-induced relaxation. These results indicate that nipradilol relaxes the rabbit ciliary artery by two different mechanisms. First, the relaxation is due to the NO produced by denitrification of nipradilol itself. Second, nipradilol may act as an alpha-adrenergic antagonist. These actions of nipradilol may explain the mechanisms of increased ocular blood flow in vivo.

Effect of latanoprost, prostaglandin F(2)alpha and nipradilol on isolated bovine ciliary muscle.

PURPOSE: Ciliary muscle tone is considered to be an important factor for control of uveoscleral outflow. In an attempt to clarify the functional roles of the ciliary muscle in uveoscleral outflow, the effects of latanoprost, prostaglandin (PG)F(2)alpha or nipradilol, all of which are known to increase uveoscleral outflow, were investigated, using the bovine ciliary muscle. METHODS: We isolated longitudinal ciliary muscle from bovine eyes and investigated the effects of these three agents on the mechanical properties of this muscle using isometric tension recording methods. RESULTS: Latanoprost and PGF(2)alpha evoked small but discrete contractions at a concentration of 0.1 microM even during the sustained contraction evoked by 10 mM acetylcholine (ACh). However, nipradilol did not evoke any response at concentrations up to 0.1 mM. None of these agents had an effect on the amplitude of the ciliary muscle twitch contraction evoked by electrical field stimulation. CONCLUSIONS: Our findings indicate that these three agents have no relaxant effect on isolated bovine ciliary muscle even during the sustained contraction evoked by ACh. Further, these agents had no effect on the contraction evoked by field stimulation, which indicates that the drugs have no presynaptic effects. These results are inconsistent with the hypothesis that drugs that increase uveoscleral outflow relax the ciliary muscle with a consequent increase in uveoscleral outflow. Further investigation of the role of ciliary muscle contractility on uveoscleral outflow is warranted.

Effect of pituitary adenylate cyclase-activating peptide on isolated rabbit iris sphincter and dilator muscles.

PURPOSE: Pituitary adenylate cyclase-activating peptide (PACAP) is a sensory neuropeptide in the eye that is released by noxious stimuli and considered to be a mediator of the neurogenic ocular injury response, including miosis. The purpose of this study was to clarify the functional role of PACAP in iris sphincter and dilator muscles. METHODS: Iris sphincter and dilator muscles were isolated from rabbit eyes, and the effect of PACAP on mechanical responses of these muscles using isometric tension-recording methods was investigated. RESULTS: The iris sphincter responded to electric field stimulation with contractions composed of fast twitch and subsequent slow components. Both PACAP 27 and PACAP 38 enhanced the twitch response, but neither had an effect on the slow response. The effect of both PACAPs on the twitch response was dose dependent. Neither PACAP had an effect on the amplitude of contraction evoked by exogenously applied Ach. For the iris dilator muscle, PACAP 27 inhibited the contractions induced by field stimulation or phenylephrine, whereas PACAP 38 had no effect. CONCLUSIONS: Both PACAP 27 and PACAP 38 enhance cholinergic transmission in sphincter muscle. The PACAP 27 induces relaxation of the dilator muscle by a direct effect on the muscle itself. The PACAP released during an ocular inflammatory response may induce miosis by the enhancement of cholinergic stimulation of the iris sphincter and by direct relaxation of the dilator muscles.