Protocol for the BAG-RECALL clinical trial: a prospective, multi-center, randomized, controlled trial to determine whether a bispectral index-guided protocol is superior to an anesthesia gas-guided protocol in reducing intraoperative awareness with explicit recall in high risk surgical patients

Background

Sevoflurane has been demonstrated to vasodilate the foeto-placental vasculature. We aimed to determine the contribution of modulation of potassium and calcium channel function to the vasodilatory effect of sevoflurane in isolated human chorionic plate arterial rings.

Methods

Quadruplicate ex vivo human chorionic plate arterial rings were used in all studies. Series 1 and 2 examined the role of the K⁺ channel in sevoflurane-mediated vasodilation. Separate experiments examined whether tetraethylammonium, which blocks large conductance calcium activated K⁺ (K_Ca++) channels (Series 1A+B) or glibenclamide, which blocks the ATP sensitive K⁺ (K_ATP) channel (Series 2), modulated sevoflurane-mediated vasodilation. Series 3 – 5 examined the role of the Ca⁺⁺ channel in sevoflurane induced vasodilation. Separate experiments examined whether verapamil, which blocks the sarcolemmal voltage-operated Ca⁺⁺ channel (Series 3), SK&F 96365 an inhibitor of sarcolemmal voltage-independent Ca⁺⁺ channels (Series 4A+B), or ryanodine an inhibitor of the sarcoplasmic reticulum Ca⁺⁺ channel (Series 5A+B), modulated sevoflurane-mediated vasodilation.

Results

Sevoflurane produced dose dependent vasodilatation of chorionic plate arterial rings in all studies. Prior blockade of the K_Ca++ and K_ATP channels augmented the vasodilator effects of sevoflurane. Furthermore, exposure of rings to sevoflurane in advance of TEA occluded the effects of TEA. Taken together, these findings suggest that sevoflurane blocks K⁺ channels. Blockade of the voltage-operated Ca⁺⁺channels inhibited the vasodilator effects of sevoflurane. In contrast, blockade of the voltage-independent and sarcoplasmic reticulum Ca⁺⁺channels did not alter sevoflurane vasodilation.

Conclusion

Sevoflurane appears to block chorionic arterial K_Ca++ and K_ATP channels. Sevoflurane also blocks voltage-operated calcium channels, and exerts a net vasodilatory effect in the in vitro foeto-placental circulation.     

Protonation,alkylation, addition and redox reactions of 16, 17 and 18 valence electron [Mo(L)(NO)('S4')] complexes [L = SPh,PMe3, NO; 'S4'2– = 1,2-Bis-(2-mercaptophenylthio)ethane(2-)]

In the quest for complexes modelling functional characteristics of metal sulfur oxidoreductases, a series of molybdenum nitrosyl complexes with sulfur-dominated coordination sphere was synthesized. Treatment of the 16, 17 and 18 valence electron (VE) complexes [Mo(L)(NO)('S₄')] (1–3) [L?=?SPh (1), PMe₃ (2), NO (3), 'S₄'^2–?=?1,2-bis-(2-mercaptophenylthio) ethane(2-)] with the Brönsted acid HBF₄ resulted in formation of different types of products. 1 and 3 were reversibly protonated at one thiolate atom of the 'S₄'^2– ligand;2, however, yielded the phosphonium salt [HPMe₃]BF₄ and the dinuclear [Mo(NO)('S₄')]₂. Alkylation of 1, 2 and 3 by Me₃OBF₄ or Et₃OBF₄ uniformly resulted in high yields of [Mo(L)(NO)(R-'S₄')]BF₄ complexes [L?=?SPh: R?=?Me (5), Et (6); L?=?PMe₃: R?=?Me (7); L?=?NO: R?=?Me (8), Et (9)] in which one thiolate atom of the 'S₄'^2– ligand had become alkylated; the NMR spectra of 5, 6, 8 and 9 indicated that only one out of four theoretically possible diastereoisomers had formed. 5 and 6 were characterized also by single-crystal X-ray structure analyses. A comparison of ν(NO) bands and redox potentials (cyclic voltammetry) of parent complexes and alkylated derivatives showed that alkylation leads to a decrease in electron density at the molybdenum center and to a positive shift in redox potentials. The 16 VE complex 1 could be reduced, also chemically, to give the corresponding 17 VE anion [1]^–, and inserted elemental sulfur into the Mo-SPh bond, forming the 18 VE phenylperthio complex [Mo(η²–SSPh)(NO)('S₄')] (11) which, upon reaction with PPh₃, gave SPPh₃ and regenerated the parent complex 1. These results are discussed with regard to the sequence of proton and electron transfer steps occurring in substrate conversions catalyzed by metal sulfur oxidoreductases.     

Hyperfine interactions and electron distribution in FeIIFeI and FeIFeI models for the active site of the [FeFe] hydrogenases: Mössbauer spectroscopy studies of low-spin FeI

Mössbauer studies of [{μ-S(CH₂C(CH₃)₂CH₂S}(μ-CO)Fe^IIFe^I(PMe₃)₂(CO)₃]PF₆ (1 _OX ), a model complex for the oxidized state of the [FeFe] hydrogenases, and the parent Fe^IFe^I derivative are reported. The paramagnetic 1 _OX is part of a series featuring a dimethylpropanedithiolate bridge, introducing steric hindrance with profound impact on the electronic structure of the diiron complex. Well-resolved spectra of 1 _OX allow determination of the magnetic hyperfine couplings for the low-spin distal Fe^I ( $ {\text{Fe}}^{\text{I}} _{\text{ D}} $ Fe D I ) site, A _x,y,z  = [?24 (6), ?12 (2), 20 (2)] MHz, and the detection of significant internal fields (approximately 2.3 T) at the low-spin ferrous site, confirmed by density functional theory (DFT) calculations. Mössbauer spectra of 1 _OX show nonequivalent sites and no evidence of delocalization up to 200 K. Insight from the experimental hyperfine tensors of the Fe^I site is used in correlation with DFT to reveal the spatial distribution of metal orbitals. The Fe–Fe bond in [Fe₂{μ-S(CH₂C(CH₃)₂CH₂S}(PMe₃)₂(CO)₄] (1) involving two $ d_{{z^{2} }} $ d z 2 -type orbitals is crucial in keeping the structure intact in the presence of strain. On oxidation, the distal iron site is not restricted by the Fe–Fe bond, and thus the more stable isomer results from inversion of the square pyramid, rotating the $ d_{{z^{2} }} $ d z 2 orbital of $ {\text{Fe}}^{\text{I}} _{\text{ D}} $ Fe D I . DFT calculations imply that the Mössbauer properties can be traced to this $ d_{{z^{2} }} $ d z 2 orbital. The structure of the magnetic hyperfine coupling tensor, A, of the low-spin Fe^I in 1 _OX is discussed in the context of the known A tensors for the oxidized states of the [FeFe] hydrogenases.     

Oxidation and reduction of sulfite contribute to susceptibility and detoxification of SO2 in Populus × canescens leaves

Key Message

The critical level for SO ₂ susceptibility of Populus × canescens is approximately 1.2 μL L ^?1 SO ₂ . Both sulfite oxidation and sulfite reduction and assimilation contribute to SO ₂ detoxification.

Abstract

In the present study, uptake, susceptibility and metabolism of SO₂ were analyzed in the deciduous tree species poplar (Populus × canescens). A particular focus was on the significance of sulfite oxidase (SO) for sulfite detoxification, as SO has been characterized as a safety valve for SO₂ detoxification in herbaceous plants. For this purpose, poplar plants were exposed to different levels of SO₂ (0.65, 0.8, 1.0, 1.2 μL L^?1) and were characterized by visible injuries and at the physiological level. Gas exchange parameters (stomatal conductance for water vapor, CO₂ assimilation, SO₂ uptake) of the shoots were compared with metabolite levels (sulfate, thiols) and enzyme activities [SO, adenosine 5′-phosphosulfate reductase (APR)] in expanding leaves (80–90 % expanded). The critical dosage of SO₂ that confers injury to the leaves was 1.2 μL L^?1 SO₂. The observed increase in sulfur containing compounds (sulfate and thiols) in the expanding leaves strongly correlated with total SO₂ uptake of the plant shoot, whereas SO₂ uptake rate was strongly correlated with stomatal conductance for water vapor. Furthermore, exposure to high concentration of SO₂ revealed channeling of sulfite through assimilatory sulfate reduction that contributes in addition to SO-mediated sulfite oxidation to sulfite detoxification in expanding leaves of this woody plant species.     

Endogenous nitric oxide generation in protoplast chloroplasts

Key message

NO generation is studied in the protoplast chloroplasts. NO, ONOO ^? and ROS (O ₂ ^? and H ₂ O ₂ ) are generated in chloroplasts. Nitric oxide synthase-like protein appears to be involved in NO generation.

Abstract

Nitric oxide stimulates chlorophyll biosynthesis and chloroplast differentiation. The present study was conducted to better understand the process of NO generation in the leaf chloroplasts and protoplasts. NO, peroxynitrite and superoxide anion were investigated in the protoplasts and isolated chloroplasts using specific dyes, confocal laser scanning and light microscopy. The level of NO was highest after protoplast isolation and subsequently decreased during culture. Suppression of NO signal in the presence of PTIO, suggests that diaminofluorescein-2 diacetate (DAF-2DA) detected NO. Detection of peroxynitrite, a reaction product of NO and superoxide anion, further suggests NO generation. Moreover, generation of NO and peroxynitrite in the chloroplasts of wild-type Arabidopsis and their absence or weak signals in the leaf-derived protoplasts of Atnoa1 mutants confirmed the reactivity of DAF-2DA and aminophenyl fluorescein to NO and peroxynitrite, respectively. Isolated chloroplasts also showed signal of NO. Suppression of NO signal in the presence of 100 μM nitric oxide synthase inhibitors [l-NNA, Nω-nitro-l-arginine and PBIT, S,S′-1,3-phenylene-bis(1,2-ethanediyl)-bis-isothiourea] revealed that nitric oxide synthase-like system is involved in NO synthesis. Suppression of NO signal in the protoplasts isolated in the presence of cycloheximide suggests de novo synthesis of NO generating protein during the process of protoplast isolation. Furthermore, the lack of inhibition of NO production by sodium tungstate (250 μM) and inhibition by l-NNA, and PBIT suggest involvement NOS-like protein, but not nitrate reductase, in NO generation in the leaf chloroplasts and protoplasts.     

Population structure and association mapping of yield contributing agronomic traits in foxtail millet

Key message

Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R ²  = 18 %) with nine agronomic traits in foxtail millet.

Abstract

Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R ² = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.     

Individual patient data meta-analysis of acupuncture for chronic pain: protocol of the Acupuncture Trialists' Collaboration

Objectives

To evaluate the use and reporting of adjusted analysis in randomised controlled trials (RCTs) and compare the quality of reporting before and after the revision of the CONSORT Statement in 2001.

Design

Comparison of two cross sectional samples of published articles.

Data Sources

Journal articles indexed on PubMed in December 2000 and December 2006.

Study Selection

Parallel group RCTs with a full publication carried out in humans and published in English

Main outcome measures

Proportion of articles reported adjusted analysis; use of adjusted analysis; the reason for adjustment; the method of adjustment and the reporting of adjusted analysis results in the main text and abstract.

Results

In both cohorts, 25% of studies reported adjusted analysis (84/355 in 2000 vs 113/422 in 2006). Compared with articles reporting only unadjusted analyses, articles that reported adjusted analyses were more likely to specify primary outcomes, involve multiple centers, perform stratified randomization, be published in general medical journals, and recruit larger sample sizes. In both years a minority of articles explained why and how covariates were selected for adjustment (20% to 30%). Almost all articles specified the statistical methods used for adjustment (99% in 2000 vs 100% in 2006) but only 5% and 10%, respectively, reported both adjusted and unadjusted results as recommended in the CONSORT guidelines.

Conclusion

There was no evidence of change in the reporting of adjusted analysis results five years after the revision of the CONSORT Statement and only a few articles adhered fully to the CONSORT recommendations.     

Synthesis of eperezolid-like molecules and evaluation of their antimicrobial activities

3-Fluoro-4-(4-phenylpiperazin-l-yl)aniline (II) prepared from 3,4-difluoro nitrobenzene was converted to the corresponding Schiff bases (III) and (IV) by treatment with 4-methoxybenzaldehyde and indol-3-carbaldehyde, respectively. Treatment of amine (II) with 4-fluorophenyl isothiocyanate afforded the corresponding thiourea derivative (V). Compound (V) was converted to thiazolidinone and thiazoline derivatives (VI) and (VII) by cyclocondensation with ethylbromoacetate or 4-chlorophenacylbromide, respectively. The synthesis of carbothioamide derivative (X) was performed starting from compound (II) by three steps. Treatment of compound (X) with sodium hydroxide, sulfuric acid, or chlorophenacyl bromide generated the corresponding 1,2,4-triazole (XI), 1,3,4-thiadiazole (XII), and 1,3-thiazolidinone (XIII) derivatives, respectively. The structural assignments of new compounds were based on their elemental analysis and spectral (IR, ¹H-NMR, ¹³C-NMR, and LC-MS) data. In the antimicrobial activity study all the compounds revealed high anti-Mycobacterium smegmatis activity.     

Soybean seed protein electrophoresis profiles from 15 Asian countries or regions: Hypotheses on paths of dissemination of soybeans from China

Soybean [Glycine max (L.) Merr.] seed protein extracts from 1,603 accessions obtained from 15 Asian countries or regions (not including Japan) were analyzed for the presence of alleles of 2 proteins. Three alleles of the Kunitz. trypsin inhibitor orSBTI-A ₂ designated asTi ^a,Ti ^b andTi ^c are electrophoretically distinguishable from one another by their different Rf values of 0.79, 0.75 and 0.83, respectively. The Sp₁ seed protein or β-amylase has 2 alleles designatedSp1 ^a andSp ₁ ^b which are electrophoretically distinguishable from one another by their Rf values 0.36 and 0.42. About 94 percent of the soybean accessions had theTi ^a allele. Two accessions from Korea,P.I. 157440 andP.I. 196168, do not have theSBTI-A2 protein(ti). Two accessions, one from Pakistan and the other from Korea, were identified as having theTi ^c allele. Only the Korean and central Indian soybean populations have a high frequency for theTi ^b allele. Within Korea, the soybeans from those districts that lie closest to Japan have a high frequency for theTi ^b allele whereas the soybeans from those districts that lie closest to China have a low frequency for theTi ^b allele. TheTi ^b allele is not present in soybeans from the Philippines, Vietnam, Thailand, Malaysia, Burma, Nepal, Pakistan, and Afghanistan. Only 1 accession each from Taiwan and Indonesia have theTi ^b allele. TheSp ₁ ^a allele is not present in soybeans from Taiwan, Vietnam, Thailand, Malaysia, Indonesia, Burma, Pakistan and Afghanistan. The highest frequency for theSp1 ^a allele occurs in soybean germ plasm from northern India and Nepal. The soybeans from Asia (including Japan) were divided into 3 gene centers— primary, secondary, and tertiary—containing 7 germ plasm pools. Paths of dissemination of the soybean from China to the rest of Asia were developed based upon a combination of electrophoretic data and available historical, agronomic, and biogeographical literature.     

Arabidopsis Brassinosteroid-overproducing gulliver3-D/dwarf4-D mutants exhibit altered responses to Jasmonic acid and pathogen

Key message

Arabidopsis gulliver3 - D/dwarf4 - D displays growth-promoting phenotypes due to activation tagging of a key brassinosteroid biosynthetic gene DWARF4. In gul3-D/dwf4-D , the Jasmonate and Salicylate signaling pathways were relatively activated and suppressed, respectively.

Abstract

Energy allocation between growth and defense is elegantly balanced to achieve optimal development in plants. Brassinosteroids (BRs), steroidal hormones essential for plant growth, are regulated by other plant hormones, including auxin and jasmonates (JA); auxin stimulates the expression of a key brassinosteroid (BR) biosynthetic gene, DWARF4 (DWF4), whereas JA represses it. To better understand the interaction mechanisms between growth and defense, we isolated a fast-growing mutant, gulliver3-D (gul3-D), that resulted from the activation tagging of DWF4, and examined the response of this mutant to defense signals, including JA, Pseudomonas syringae pv. tomato (Pst DC3000) infection, and wounding. The degree of root growth inhibition following MeJA treatment was significantly decreased in gul3-1D/dwf4-5D relative to the wild type, suggesting that JA signaling is partially desensitized in gul3-1D. Quantitative RT-PCR analysis of the genes involved in JA and salicylic acid (SA) responses, including MYC2, PDF1.2, CORI3, PR1, and PR2, revealed that JA signaling was preferentially activated in gul3-1D, whereas SA signaling was suppressed. As a result, gul3-1D was more susceptible to a biotrophic pathogen, Pst DC3000. Based on our results, we propose a model in which BR and JA cooperate to balance energy allocation between growth and defense responses. In ambient conditions, BRs promote plant growth; however, when stresses trigger JA signaling, JA compromises BR signaling by downregulating DWF4 expression.     

Apoplastic calmodulin promotes self-incompatibility pollen tube growth by enhancing calcium influx and reactive oxygen species concentration in Pyrus pyrifolia

Key message

This study indicated that Ca ²⁺ , ROS and actin filaments were involved with CaM in regulating pollen tube growth and providing a potential way for overcoming pear self-incompatibility.

Abstract

Calmodulin (CaM) has been associated with various physiological and developmental processes in plants, including pollen tube growth. In this study, we showed that CaM regulated the pear pollen tube growth in a concentration-dependent bi-phasic response. Using a whole-cell patch-clamp configuration, we showed that apoplastic CaM induced a hyperpolarization-activated calcium ion (Ca²⁺) current, and anti-CaM largely inhibited this type of Ca²⁺ current. Moreover, upon anti-CaM treatment, the reactive oxygen species (ROS) concentration decreased and actin filaments depolymerized in the pollen tube. Interestingly, CaM could partially rescue the inhibition of self-incompatible pear pollen tube growth. This phenotype could be mediated by CaM-enhanced pollen plasma membrane Ca²⁺ current, tip-localized ROS concentration and stabilized actin filaments. These data indicated that Ca²⁺, ROS and actin filaments were involved with CaM in regulating pollen tube growth and provide a potential way for overcoming pear self-incompatibility.     

Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata

Key message

An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time.

Abstract

An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq^TM markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.     

Estimating the absorptive root area in Norway spruce by using the common direct and indirect earth impedance methods

Aims

Estimates of root absorption magnitude are needed for the balanced management of forest ecosystems, but no methods able to work on the whole tree and stand level were available. Modified earth impedance method was developed recently and here it was tested, by comparing the results with those obtained by combination of several classical methods.

Methods

We used direct (soil cores, scanning and microscopy) and indirect (sap flow patterns and modified earth impedance) methods in an attempt to estimate the absorptive root area indexes (RAI) at two sites of about 25 and 40-years-old Norway spruce. We considered the geometric surfaces of all scanned fine roots to be equal to the fine root absorptive area (RAI _scan ). To estimate the potentially physically permeable area of fine roots, we microscopically evaluated the point of secondary xylem appearance and calculated the geometric area of root portions with primary structure (RAI _micro ). We termed the area of electrically conductive root surface as the active (ion) absorptive area (RAI _mei ) and measured its extent by the modified earth impedance (MEI) method.

Results

The highest values for absorptive root areas at the two experimental sites we obtained with the scanning method (RAI _scan was considered to be 100%), followed by the RAI _micro (51%) and RAI _mei (32%). RAImei reached about 2/3 of RAImicro. The surface area of the ectomycorrhizal hyphae was an order of magnitude larger than that of all fine roots, but the MEI did not measure such increase.

Conclusions

We showed that the absorptive root area, indirectly estimated by the MEI, provides consistent results that approach the values obtained for fine roots with a primary structure estimated by traditional direct methods. The similar range of the values for the absorptive root surface area obtained by microscopy and by the MEI method indicates that this method is feasible and that it could be used to determine the extent of active absorptive root surface areas in forests.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

Synthesis of 1,6-Diaryl-5,7-dioxo(dithio)imidazo[1,2-a] [1,3,5]triazines. A Novel Pathway for Imidazo[1,2-a] [1,3,5]triazine Systems Obtained via 1-(Imidazolin-2-yl)urea and Thiourea Derivatives

Novel 1,6-diaryl-5,7(1H)dioxo(dithio)-2,3-dihydroimidazo[1,2-a][1, 3, 5]triazines 8, and 9 were synthesized by cyclization of the respective 1-(imidazolin-2-yl)ureas 4 or thioureas 6 with phosgene or thiophosgene in the presence of bases. 1-Aryl-2-aminoimidazolines 1 reacting with arylisocyanates 2 or arylisothiocyanates 3 form a mixture of isomeric imidazolin-2-yl 4 and 6 and imidazolin-3-yl 5 and 7 urea or thiourea derivatives. Isomers 4 and 6 can be easily separated and used for the cyclization reaction. The structures of the main intermediates and the final target compounds were confirmed by ¹H-NMR spectral analysis. Discussion of the possible course of the reactions is also presented.     

Relating normal vibrational modes to local vibrational modes: benzene and naphthalene

Local vibrational modes can be directly derived from normal vibrational modes using the method of Konkoli and Cremer (Int J Quant Chem 67:29, 1998). This implies the calculation of the harmonic force constant matrix F ^q (expressed in internal coordinates q) from the corresponding Cartesian force constant matrix f ^x with the help of the transformation matrix U?=?WB ^?(BWB ^?)^?1 (B: Wilson’s B-matrix). It is proven that the local vibrational modes are independent of the choice of the matrix W. However, the choice W?=?M ^?1 (M: mass matrix) has numerical advantages with regard to the choice W?=?I (I: identity matrix), where the latter is frequently used in spectroscopy. The local vibrational modes can be related to the normal vibrational modes in the form of an adiabatic connection scheme (ACS) after rewriting the Wilson equation with the help of the compliance matrix. The ACSs of benzene and naphthalene based on experimental vibrational frequencies are discussed as nontrivial examples. It is demonstrated that the local-mode stretching force constants provide a quantitative measure for the C–H and C–C bond strength.     

Purple-leaved Ficus lyrata plants produced by overexpressing a grapevine VvMybA1 gene

Key message

This study established an efficient method of regenerating plants of Ficus lyrata and producing purple-leaved F. lyrata plants through genetic transformation using a VvMybA1 gene of grapevine.

Abstract

Ficus lyrata, a species with unique violin- or guitar-shaped leaves, was regenerated from leaf-derived calli cultured on Murashige and Skoog (MS) basal medium supplemented with 4.5 μM N-phenyl-N’-1, 2, 3-thiadiazol-5-yl urea (TDZ) and 0.5 μM α-naphthalene acetic acid (NAA). Leaf discs were inoculated with Agrobacterium tumefaciens strain EHA 105 harboring a binary vector DEAT that contains the VvMybA1 gene and neomycin phosphotransferase (npt II) gene and subsequently cultured on the established regeneration medium supplemented with 100 mg l^?1 kanamycin. Results showed that 87.5 % of the leaf discs produced kanamycin-resistant callus, and 68.8 % of them produced adventitious shoots. Transgenic plants with three leaf colors including green, green-purple, and purple were produced. Regular and quantitative real-time PCR analyses confirmed the integration of transgenes into the host genome. Semi-quantitative RT-PCR analysis indicated that the VvMybA1 gene was responsible for the purple-colored phenotype. Purple-leaved plants with strong color stability grew vigorously in a greenhouse. This study illustrated the feasibility of using a genetically engineered VvMybA1 gene for drastic modification of leaf color of an important woody ornamental plant.     

Figure text extraction in biomedical literature

Background

Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org) to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures.

Methodology

We first evaluated an off-the-shelf Optical Character Recognition (OCR) tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT) to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons.

Results/Conclusions

The evaluation on 382 figures (9,643 figure texts in total) randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for text extraction. In addition, our results show that FigTExT can extract texts that do not appear in figure captions or other associated text, further suggesting the potential utility of FigTExT for improving figure search.Open in a separate windowFigure 9Additional reasons for OCR errors.(A) High image complexity. (B) Thick stroke. (C) Low image contrast. (D) Small font size. (E) Non-standard font type.