Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ~50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction. Database URL: http://www.cellfinder.org

CellFinder: a cell data repository

CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder's data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder's web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians

A COMPARATIVE STUDY OF UNIVARIATE TIME SERIES MODELLING FOR NATURAL RUBBER PRODUCTION IN MALAYSIA

Malaysia is one of the top countries that produces natural rubber and was ranked sixth place globally. The earnings from natural rubber products are making billions of ringgit for the country. However, over the past years the natural rubber production in Malaysia has been inconsistent and the deficiencies in the production can affect Malaysia’s economy. Therefore, it is important for relevant agencies and departments to understand the patterns and trends of natural rubber production in Malaysia besides having the ability to forecast. Hence, the integrated autoregressive moving average (ARIMA), seasonal autoregressive moving average (SARIMA) and the seasonal Holt-Winter’s model were being considered for the purpose of modelling and forecasting this study. The forecast accuracy criteria used to evaluate the performance of the models are the root mean square error (RMSE) and mean absolute percentage error (MAPE). The results showed that the seasonal Holt-Winter’s model appeared to be the best model as it yielded the lowest RMSE and MAPE values. The seasonal Holt-Winter’s model, however, is not a good choice of model as it was unable to forecast six months ahead values. On the other hand, the SARIMA model had a better forecast ability when forecasting the values for the same duration. Therefore, the SARIMA model is taken to be the model in forecasting the natural rubber production in Malaysia for that period. This study has shown that the best fit model that fulfil all the forecast accuracy criteria may not have the best forecast ability

Prenatal antidepressant exposure associated with CYP2E1 DNA methylation change in neonates

Some but not all neonates are affected by prenatal exposure to serotonin reuptake inhibitor antidepressants (SRI) and maternal mood disturbances. Distinguishing the impact of these 2 exposures is challenging and raises critical questions about whether pharmacological, genetic, or epigenetic factors can explain the spectrum of reported outcomes. Using unbiased DNA methylation array measurements followed by a detailed candidate gene approach, we examined whether prenatal SRI exposure was associated with neonatal DNA methylation changes and whether such changes were associated with differences in birth outcomes. Prenatal SRI exposure was first associated with increased DNA methylation status primarily at CYP2E1(βNon-exposed = 0.06, βSRI-exposed = 0.30, FDR = 0); however, this finding could not be distinguished from the potential impact of prenatal maternal depressed mood. Then, using pyrosequencing of CYP2E1 regulatory regions in an expanded cohort, higher DNA methylation status both the mean across 16 CpG sites (P < 0.01) and at each specific CpG site (P < 0.05) was associated with exposure to lower 3rd trimester maternal depressed mood symptoms only in the SRI-exposed neonates, indicating a maternal mood x SRI exposure interaction. In addition, higher DNA methylation levels at CpG2 (P = 0.04), CpG9 (P = 0.04) and CpG10 (P = 0.02), in the interrogated CYP2E1 region, were associated with increased birth weight independently of prenatal maternal mood, SRI drug exposure, or gestational age at birth. Prenatal SRI antidepressant exposure and maternal depressed mood were associated with altered neonatal CYP2E1 DNA methylation status, which, in turn, appeared to be associated with birth weight

Nest Architecture, Colony Productivity, and Duration of Immature Stages in a Social Wasp, Mischocyttarus consimilis

This study examined the nest architecture, colony productivity, and duration of the immature stages of the social wasp Mischocyttarus consimilis Zikáán (Hymenoptera: Vespidae). The study was carried out under field conditions. Nests of M. consimilis consist of a single uncovered comb, which is attached to the substratum by a single petiole. The data for the nest architecture showed a positive and significant correlation between the size of the comb and the diameter of the petiole, and also between the height and diameter of the cells. The nests were constructed on horizontal, vertical, and sloping substrata with no apparent preference for a specific orientation. The colonies produced 72.9 cells and 40.7 adults on average. The mean frequency of productive cells was 33.3%, and 19.4% of the cells were reused. The mean duration of the immature stages combined was 69.7 days and the egg, larval, and pupal stages had mean durations of 14.9, 36.0, and 18.8 days, respectively. The duration of each immature stage was significantly shorter in the warmhumid season, and the larval and pupal stages were shorter during the colony pre-emergence stage

Mitigating street flooding with permeable structures: A modelling case study

This paper describes the modelling efforts of placing a permeable street adjacent to flash-flood-causing urban drain so that overflowing floodwaters from the drain could be absorbed by water storage structure under the street. Three types of permeable structures were included in the modelling with porosities of 23, 63 and 86 % representing low, medium and high storage volumes, respectively. By using the Storm Water Management Model developed by the US Environmental Protection Agency, the properties of the three types of permeable structures were implemented in models imitating a commercial center and its drainage system, as a case study. The permeable street was modelled as part of the drainage system, in contrast to conventional roads rarely modelled as such. Local rainfall patterns were then used with the models of the case study, in which water flow characteristics of the drainage systems with and without the permeable structures were analyzed. The first type that involved conventional pavers and aggregates had the least water detention time of 2 hours. The second type that consisted of modular precast concrete units held the water for 5 hours; and the third type that was cast-in-place concrete tank system held the water longer for 6 hours. The longer the time floodwater is detained within a permeable structure, the better the mitigating effects of the street flooding. The second and third types of structures were more promising than the first type. However, choosing either second type or third type would be a case-by-case decision, considering various factors of the flash flood

On the selection and design of proteins and peptide derivatives for the production of photoluminescent, red-emitting gold quantum clusters

Novel pathways of the synthesis of photoluminescent gold quantum clusters (AuQCs) using biomolecules as reactants provide biocompatible products for biological imaging techniques. In order to rationalize the rules for the preparation of red-emitting AuQCs in aqueous phase using proteins or peptides, the role of different organic structural units was investigated. Three systems were studied: proteins, peptides, and amino acid mixtures, respectively. We have found that cysteine and tyrosine are indispensable residues. The SH/S-S ratio in a single molecule is not a critical factor in the synthesis, but on the other hand, the stoichiometry of cysteine residues and the gold precursor is crucial. These observations indicate the importance of proper chemical behavior of all species in a wide size range extending from the atomic distances (in the AuI-S semi ring) to nanometer distances covering the larger sizes of proteins assuring the hierarchical structure of the whole self-assembled system

Epilepsie chez les Enfants Atteints d’Infirmité Motrice Cérébrale : à Propos de 412 Observations à Yaoundé, Cameroun

Une &eacute;tude prospective, descriptive et cons&eacute;cutive r&eacute;alis&eacute;e &agrave; l&rsquo;Unit&eacute; de Neurologie P&eacute;diatrique de l&rsquo;h&ocirc;pital gyn&eacute;co-obst&eacute;trique et p&eacute;diatrique de Yaound&eacute; (Cameroun) du 1er janvier 2004 au 31 D&eacute;cembre 2008 a permis de retenir 412 patients admis pour infirmit&eacute; motrice c&eacute;r&eacute;brale (IMC). L&rsquo;IMC repr&eacute;sentait 20,39% des pathologies neurop&eacute;diatriques. L&rsquo;&acirc;ge moyen des patients &eacute;tait de 31,7 mois. Les &eacute;tiologies ant&eacute;natales &eacute;taient de (5,51%), p&eacute;rinatales (65,25%), postnatales (29,22%) ; elles &eacute;taient domin&eacute;es par l&rsquo;asphyxie n&eacute;onatale (43,68% de cas). L&rsquo;&eacute;pilepsie &eacute;tait l&rsquo;une des principales affections associ&eacute;es &agrave; L&rsquo;IMC. Elle &eacute;tait retrouv&eacute;e chez 41,5% des patients. L&rsquo;&eacute;pilepsie &eacute;tait plus fr&eacute;quente dans la t&eacute;trapl&eacute;gie spastique et l&rsquo;h&eacute;mipl&eacute;gie c&eacute;r&eacute;brale infantile. Par ailleurs 68,72% de patients ont fait la premi&egrave;re crise &eacute;pileptique au cours de leur premi&egrave;re ann&eacute;e de vie. Les convulsions n&eacute;onatales, l&rsquo;asphyxie n&eacute;onatale et les infections n&eacute;onatales ont &eacute;t&eacute; les facteurs de risque pr&eacute;disposant les enfants avec IMC &agrave; faire l&rsquo;&eacute;pilepsie.Mots Cl&eacute;s enfants ; infirmit&eacute; motrice c&eacute;r&eacute;brale ; &eacute;pilepsie ; Camerou

Aharonov-Bohm interferences from local deformations in graphene

One of the most interesting aspects of graphene is the tied relation between structural and electronic properties. The observation of ripples in the graphene samples both free standing and on a substrate has given rise to a very active investigation around the membrane-like properties of graphene and the origin of the ripples remains as one of the most interesting open problems in the system. The interplay of structural and electronic properties is successfully described by the modelling of curvature and elastic deformations by fictitious gauge fields that have become an ex- perimental reality after the suggestion that Landau levels can form associated to strain in graphene and the subsequent experimental confirmation. Here we propose a device to detect microstresses in graphene based on a scanning-tunneling-microscopy setup able to measure Aharonov-Bohm inter- ferences at the nanometer scale. The interferences to be observed in the local density of states are created by the fictitious magnetic field associated to elastic deformations of the sample.Comment: Some bugs fixe

Room-temperature ferromagnetism in graphite driven by 2D networks of point defects

Ferromagnetism in carbon-based materials is appealing for both applications and fundamental science purposes because carbon is a light and bio-compatible material that contains only s and p electrons in contrast to traditional ferromagnets based on 3d or 4f electrons. Here we demonstrate direct evidence for ferromagnetic order locally at defect structures in highly oriented pyrolytic graphite (HOPG) with magnetic force microscopy and in bulk magnetization measurements at room temperature. Magnetic impurities have been excluded as the origin of the magnetic signal after careful analysis supporting an intrinsic magnetic behavior of carbon. The observed ferromagnetism has been attributed to originate from unpaired electron spins localized at grain boundaries of HOPG. Grain boundaries form two-dimensional arrays of point defects, where their spacing depends on the mutual orientation of two grains. Depending on the distance between these point defects, scanning tunneling spectroscopy of grain boundaries showed two intense split localized states for small distances between defects (< 4 nm) and one localized state at the Fermi level for large distances between defects (> 4 nm).Comment: 19 pages, 5 figure