Groundwater flow traced by bomb pulses of ³⁶Cl and tritiogenic ³He in a borehole

In 2001, a borehole was drilled to 400 m depth below the ground surface of a tableland in northern Japan, where horizontal porous sedimentary rock strata are deposited. Fresh drill-core and groundwater samples were collected from the borehole for estimating global fallout bomb pulses of ³H, which becomes tritiogenic ³He (tri³He) through β-decay, and ³⁶Cl. In the northern hemisphere, the maximum fallout deposition of ³⁶Cl from nuclear testing was observed during 1954–1957, and that of ³H in 1963. Most ³H (half-life 12.3 y) in the rock porewater had decayed to tri³He during the 38 years between 1963 and 2001. In the borehole, bomb pulses were observed in profiles of tri³He and ³⁶Cl/Cl at 101 m and around 138 m depth below the ground surface, respectively. The downward groundwater velocity was estimated to be 2.9–3.1 m/y from the depth of the ³⁶Cl/Cl bomb pulse and 2.7 m/y from the depth of the tri³He bomb pulse. Although the two velocity estimates differ by 10–15%, it is possible to model groundwater flow in the tableland as downward piston flow without diffusion

An analysis of gene/protein associations at PubMed scale

<p>Abstract</p> <p>Background</p> <p>Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information extraction. This work includes efforts applying event extraction methods to the entire PubMed literature database, far beyond the narrow subdomains of biomedicine for which annotated resources for extraction method development are available.</p> <p>Results</p> <p>In the present study, our aim is to estimate the coverage of all statements of gene/protein associations in PubMed that existing resources for event extraction can provide. We base our analysis on a recently released corpus automatically annotated for gene/protein entities and syntactic analyses covering the entire PubMed, and use named entity co-occurrence, shortest dependency paths and an unlexicalized classifier to identify likely statements of gene/protein associations. A set of high-frequency/high-likelihood association statements are then manually analyzed with reference to the GENIA ontology.</p> <p>Conclusions</p> <p>We present a first estimate of the overall coverage of gene/protein associations provided by existing resources for event extraction. Our results suggest that for event-type associations this coverage may be over 90%. We also identify several biologically significant associations of genes and proteins that are not addressed by these resources, suggesting directions for further extension of extraction coverage.</p

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers

Record of ³H and ³⁶Cl from the Fukushima nuclear accident recovered from soil water in the unsaturated zone at Koriyama

The opportunity to measure the concentrations of ³H and ³⁶Cl released by the Fukushima nuclear accident in 2011 directly in rain was lost in the early stage of the accident. We have, however, been able to reconstruct the deposition record of atmospheric ³H and ³⁶Cl following the accident using a bore hole that was drilled in 2014 at Koriyama at a distance of 60 km from the accident. The contributions of ³H and ³⁶Cl from the accident are 1.4 × 10¹³ and 2.0 × 10¹² atoms m⁻² respectively at this site. Very high concentrations of both ³H (46 Bq L⁻¹) and ³⁶Cl (3.36 × 10¹¹ atoms L⁻¹) were found in the unsaturated soil at depths between 300 and 350 cm. From these, conservative estimates for the ³H and ³⁶Cl concentrations in the precipitation in the ～ 6 weeks following the accident were 607 Bq L⁻¹ and 4.74 × 10¹⁰ atoms L⁻¹, respectively. A second hole drilled in 2016 showed that ³H concentrations in the unsaturated soil and shallow groundwater had returned to close to natural levels, although the ³⁶Cl concentrations were still significantly elevated above natural levels

Effects of Interval Time of the Epley Manoeuvre

Objective: The Epley maneuver (EM) has an immediate effect: rapid reduction of positional nystagmus. Benign paroxysmal positional vertigo (BPPV) causes BPPV fatigue, which constitutes fatigability of positional nystagmus and vertigo with repeated performance of the Dix-Hallpike test; notably, BPPV fatigability becomes ineffective over time. We hypothesized that the immediate effect of the EM is caused by BPPV fatigue. Therefore, we suspected that performance of the EM with intervals between head positions would worsen the immediate reduction of positional nystagmus in patients with BPPV, because BPPV fatigability would become ineffective during performance of this therapy. Methods: Forty patients with newly diagnosed BPPV were randomly assigned to the following two groups; one group performed the EM without intervals between positions (group A), and the other group performed the EM with 3 min intervals between positions (group B). The primary outcome measure was the ratio of maximum slow-phase eye velocity (MSPEV) of positional nystagmus soon after the EM, compared with that measured before the EM. Secondary outcome included whether a 30 min interval after the EM enabled recovery of MSPEV of positional nystagmus to the original value. This study followed the CONSORT 2010 reporting standards. Results: In both groups A and B, the immediate effect of the EM could be observed, because MSPEV during the second Dix-Hallpike test was significantly smaller than MSPEV during the first Dix-Hallpike test (p < 0.0001 in group A, p < 0.0001 in group B). The primary outcome measure was larger in group B than in group A (p = 0.0029). The immediate effect faded 30 min later (secondary outcome). Conclusions: This study showed that the EM had an immediate effect both with and without interval time in each head position of the EM. Because setting interval time in each head position of the EM reduced the immediate effect of the EM, interval time during the EM adds less benefit. This finding can reduce the effort exerted by doctors, as well as the discomfort experienced by patients with pc-BPPV, during EM. However, this immediate effect may be caused by BPPV fatigue, and may fade rapidly

New challenges for text mining: mapping between text and manually curated pathways

<p>Abstract</p> <p>Background</p> <p>Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge.</p> <p>Results</p> <p>To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus.</p> <p>Conclusions</p> <p>We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.</p

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

MOTIVATION: Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences. RESULTS: We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. AVAILABILITY: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/

Clinical and Pathological Improvement in Stroke-Prone Spontaneous Hypertensive Rats Related to the Pleiotropic Effect of Cilostazol

Background and Purpose-Cerebral infarction is a major cause of death or decreasing activities of daily living. This study aimed to investigate the efficacy of commonly used antiplatelet drugs on stroke and motor and cognitive functions in relation to oxidative stress markers and insulin-like growth factor 1 receptor (IGF-1R). Methods-Stroke-prone spontaneously hypertensive rats were treated with vehicle, aspirin, clopidogrel, and cilostazol from 8 to 10 weeks of age. Physiological parameters, regional cerebral blood flow, and serum lipids were examined. Motor and cognitive functions were evaluated weekly by the Rotorod and water maze task. Spontaneous infarct volume, oxidative stress markers for lipid, protein, and DNA at the ischemic boundary zone of spontaneous infarction, and the IGF-1R-positive cell ratio in the hippocampus were immunohistochemically examined in brain sections. IGF-1R beta expression in the hippocampus was assessed by Western blotting. Results-The antiplatelet drugs, cilostazol and clopidogrel, reduced the spontaneous infarct volume more than aspirin. Only cilostazol improved motor and cognitive functions with a significant increase (P<0.05) in the memory-related IGF-1R-positive ratio and IGF-1R beta expression in the hippocampus. Cilostazol reduced the 4 oxidative stress markers in affected neurons in stroke-prone spontaneously hypertensive rats regardless of blood pressure, regional cerebral blood flow, or serum lipid levels. Conclusions-The present results suggest that a possible pleiotropic effect of cilostazol resulted in the reduction of spontaneous infarct volume and preservation of motor and spatial cognitive functions. The increase of IGF-1R-positive cells in the hippocampal CA1 region could partly explain the preservation of spatial cognitive function in stroke-prone spontaneously hypertensive rats