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

Origin and hydrodynamics of xylem sap in tree stems, and relationship to root uptake of soil water

Although 10 years have passed since Japan's Fukushima nuclear accident, the future radiation risk from ¹³⁷Cs contamination of wood via root uptake is a serious concern. We estimated the depth at which the roots of evergreen coniferous sugi (Cryptomeria japonica) and broadleaf deciduous konara (Quercus serrata) trees actively take up soil water by using positive δD values from the artificial D₂O tracer and seasonal changes in the δ¹⁸O values of soil water as a natural environmental tracer. We compared the tracer concentration changes in xylem sap with those in the soil water and ascertained that both tree species primarily took up water from a depth of 20 cm, though with mixing of water from other depths. Using sap hydrodynamics in tree stems, we found that water circulation was significantly slower in heartwood than in sapwood. Heartwood water was not supplied by direct root uptake of soil water. The measured diffusion coefficients for D₂O, K⁺, Cs⁺, and I⁻ in xylem stems were greater in sapwood than in heartwood, and their magnitude was inversely correlated with their molecular weights. The distribution of D₂O and ¹³⁷Cs concentrations along the radial stem could be explained by simulations using the simple advective diffusion model

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

Jedinstveni obrazac djelovanja bisfenola A na ekspresiju gena čimbenika rasta živca embrionske mišje stanične linije N-44 dobivene iz hipotalamusa

We investigated the toxicity of bisphenol A (BPA) by determining the gene expression of nerve growth factor (Ngf) in the embryonic mouse cell line mHypoE-N44 derived from the hypothalamus exposed to BPA dose range between 0.02 and 200 μmol L-1 for 3 h. Ngf mRNA levels decreased in a dose-dependent manner, with significant reductions observed in the 2 to 50 μmol L-1 BPA treatment groups compared to controls. However, at 100 to 200 μmol L-1 the Ngf mRNA gradually increased and was significantly higher than control, while the expression of the apoptosis-related genes Caspase 3 and transformation-related protein 73 decreased significantly. These results suggest that in an embryonic hypothalamic cell line the higher doses of BPA induce a unique pattern of Ngf gene expression and that BPA has the potential to suppress apoptosis essential for early-stage brain development.U istraživanju toksičnosti bisfenola A (BPA) utvrđena je ekspresija gena čimbenika rasta živca (eng. nerve growth factor - NGF) embrionske mišje stanične linije mHypoE-N44 dobivene iz hipotalamusa nakon trosatnog izlaganja BPA-u u rasponu doza od 0,02 do 200 μmol L-1. Razine Ngf mRNA snizile su se ovisno o dozi, a značajne razlike od kontrolne skupine zamijećene su za raspon od 2 do 50 μmol L-1. Međutim, počevši od doze od 100 do 200 μmol L-1, razine Ngf mRNA značajno su se povećale u odnosu na kontrolu, a ekspresija gena kaspaze 3 i transformacijskog proteina 73 značajno snizila. Ti rezultati upućuju na to da visoke doze BPA u embrionskoj hipotalamičkoj staničnoj liniji stvaraju jedinstveni obrazac ekspresije gena Ngf te da BPA može suprimirati apoptozu koja je nužna za rani razvoj mozga