bluuebunny/crossref_metadata_2025 huggingface dataset:
A semi-quantitative enzyme-linked immunosorbent assay for Rathayibacter toxicus, the bacterium involved in annual ryegrass toxicity, to assist in risk assessment of fodder for domestic use
Authors: Masters A. M. , Samarasinghe B. , Kalkhoven M. , den Hollander L. , Palmer D. G.
Published: November 2014

A semi-quantitative enzyme-linked immunosorbent assay (ELISA) for the detection of Rathayibacter toxicus in hay or pasture was used to estimate the degree of R. toxicus bacterial gall contamination in hay or pasture that was unsuitable for export but that may be suitable for feeding to domestic livestock. Based on experience of testing of fodder samples from pastures where livestock showed clinical signs, or outbreaks of annual ryegrass toxicity (ARGT), four relevant levels of bacterial gall contamination were selected. Several 1-kg samples of hay with no contamination by R. toxicus were spiked with these four different amounts of bacterial galls to provide five different risk categories considered relevant to the occurrence of ARGT. Extracts of the spiked samples were assayed to determine the range of ELISA results to be expected in each category. To validate these risk categories, all cases of ARGT diagnosed between 2000 and 2012 by the Animal Health Laboratories, Department of Agriculture and Food Western Australia, associated with the submission of suspected toxic fodder were allocated to the risk categories on the basis of the recorded results for fodder. In ~15% and 79% of all cases, the fodder associated with outbreaks of ARGT fell into the ‘moderate risk’ and ‘high risk’ categories, respectively. The selected categories were considered to provide realistic estimations of the risk that fodder within them might cause ARGT if fed to livestock. This risk-level reporting has been adopted to enable informed decision making as to whether feeding a particular batch of hay or fodder to animals represents an acceptable risk.
Genotypic and environmental variation in seed nutraceutical and industrial composition of non-transgenic soybean (Glycine max) genotypes
Authors: Carrera Constanza S. , Dardanelli Julio L. , Soldini Diego O.
Published: November 2014

Genotype × environment interactions (G × E) induce differential response of soybean (Glycine max (L.) Merr.) genotypes to variable environmental conditions with respect to seed composition, and this may hinder breeding progress. The objectives of this study were to estimate the contribution of genotype, environment and G × E to seed chemical composition variability, and to identify the most stable non-transgenic genotypes for several chemical components. Seeds from six non-transgenic soybean genotypes that were grown in 23 environments in Argentina (24–38°S) were analysed. Although environment was the most important source affecting variation for most of the analysed chemical components, genotype and G × E also had a significant effect (P < 0.001). Stable genotypes with superior performance across a wide range of environments were ALIM3.20 for protein, linolenic acid (Len), Len : linoleic acid (LA) ratio (Len/LA), δ-tocopherol (δT) and total isoflavones (TI); ALIM4.13 for protein, oleic acid, α-tocopherol (αT) and δT; ALIM3.14 for Len, αT and TI; Ac0124-1 for Len and Len/LA; and Ac0730-3 for αT. Non-transgenic genotypes with stable chemical profile across environments would perform well under a wide range of environmental conditions for any chemical compound. This study contributes knowledge for breeders to use these genotypes to broaden the genetic backgrounds of currently available commercial cultivars, or to design production strategies that employ the genotypes directly as raw material.
Comparative analyses of cadmium and zinc uptake correlated with changes in natural resistance-associated macrophage protein (NRAMP) expression in Solanum nigrum L. and Brassica rapa
Authors: Song Y. , Hudek L. , Freestone D. , Puhui J. , Michalczyk A. A. , Senlin Z. , Ackland M. L.
Published: November 2014

Environmental context
Soils contaminated with metals can pose both environmental and human health risks. This study showed that a common crop vegetable grown in the presence of cadmium and zinc readily accumulated these metals, and thus could be a source of toxicity when eaten. The work highlights potential health risks from consuming crops grown on contaminated soils.

Abstract
Ingestion of plants grown in heavy metal contaminated soils can cause toxicity because of metal accumulation. We compared Cd and Zn levels in Brassica rapa, a widely grown crop vegetable, with that of the hyperaccumulator Solanum nigrum L. Solanum nigrum contained 4 times more Zn and 12 times more Cd than B. rapa, relative to dry mass. In S. nigrum Cd and Zn preferentially accumulated in the roots whereas in B. rapa Cd and Zn were concentrated more in the shoots than in the roots. The different distribution of Cd and Zn in B. rapa and S. nigrum suggests the presence of distinct metal uptake mechanisms. We correlated plant metal content with the expression of a conserved putative natural resistance-associated macrophage protein (NRAMP) metal transporter in both plants. Treatment of both plants with either Cd or Zn increased expression of the NRAMP, with expression levels being higher in the roots than in the shoots. These findings provide insights into the molecular mechanisms of heavy metal processing by S. nigrum L. and the crop vegetable B. rapa that could assist in application of these plants for phytoremediation. These investigations also highlight potential health risks associated with the consumption of crops grown on contaminated soils.
Automatic estimation of wheat grain morphometry from computed tomography data
Authors: Strange Harry , Zwiggelaar Reyer , Sturrock Craig , Mooney Sacha J. , Doonan John H.
Published: November 2014

Wheat (Triticum aestivum L.) grain size and morphology are playing an increasingly important role as agronomic traits. Whole spikes from two disparate strains, the commercial type Capelle and the landrace Indian Shot Wheat, were imaged using a commercial computed tomography system. Volumetric information was obtained using a standard back-propagation approach. To extract individual grains within the spikes, we used an image processing pipeline that included adaptive thresholding, morphological filtering, persistence aspects and volumetric reconstruction. This is a fully automated, data-driven pipeline. Subsequently, we extracted several morphometric measures from the individual grains. Taking the location and morphology of the grains into account, we show distinct differences between the commercial and landrace types. For example, average volume is significantly greater for the commercial type (P = 0.0024), as is the crease depth (P = 1.61 × 10−5). This pilot study shows that the fully automated approach described can retain developmental information and reveal new morphology information at an individual grain level.
Endothelin as a local regulating factor in the bovine oviduct
Authors: Yamamoto Yuki , Kohka Misa , Kobayashi Yoshihiko , Woclawek-Potocka Izabela , Okuda Kiyoshi
Published: November 2014

Endothelin (EDN) is a possible regulating factor of oviductal motility, which is important for the transport of gametes and embryo. To clarify the factors that control the secretion of EDN in the bovine oviduct, the expression of EDNs, EDN-converting enzymes (ECEs) and EDN receptors (EDNRs) were investigated. All isoforms of EDN (EDN1–3), ECE (ECE1 and ECE2) and EDNR (EDNRA and EDNRB) were immunolocalised in the epithelial cells of the ampulla and the isthmus. EDNRs were also immunolocalised in smooth-muscle cells. The mRNA expression of EDN2 and ECE2 was higher in cultured ampullary oviductal epithelial cells than in isthmic cells. The expression of EDN1, EDN2 and ECE2 in the ampullary tissue was highest on the day of ovulation. Oestradiol-17β increased EDN2 and ECE1 expression, while progesterone increased only ECE1 expression in cultured ampullary epithelial cells. These results indicate that EDNs are produced by epithelial cells and their target site is smooth-muscle and epithelial cells, and suggest that ovarian steroids are regulators of endothelin synthesis in ampullary oviductal epithelial cells.
Long-range enhancer activity determines
Myc
sensitivity to Notch inhibitors in T cell leukemia
Authors: Yashiro-Ohtani Yumi , Wang Hongfang , Zang Chongzhi , Arnett Kelly L. , Bailis Will , Ho Yugong , Knoechel Birgit , Lanauze Claudia , Louis Lumena , Forsyth Katherine S. , Chen Sujun , Chung Yoonjie , Schug Jonathan , Blobel Gerd A. , Liebhaber Stephen A. , Bernstein Bradley E. , Blacklow Stephen C. , Liu Xiaole Shirley , Aster Jon C. , Pear Warren S.
Published: November 2014

Significance

The protooncogene c-Myc (Myc) is an oncogenic driver in many cancers, but is difficult to target directly with drugs. An alternative strategy is to use drugs that inhibit factors that regulate
Myc
expression. Notch drives
Myc
expression in most T-cell leukemias, but clinical trials of Notch inhibitors have been disappointing, possibly because cells emerge that express
Myc
in a Notch-independent fashion. Here we identify the genomic switches that regulate
Myc
expression in the Notch-inhibitor–sensitive and –resistant states. Our findings suggest that Notch inhibitor resistance occurs through a “switch swap” that relieves Notch dependency while increasing dependency on a different factor, bromodomain containing 4 (Brd4). These studies provide a rationale for targeting
Myc
in T cell leukemias with combinations of Notch and Brd4 inhibitors.
Maresin 1 biosynthesis during platelet–neutrophil interactions is organ-protective
Authors: Abdulnour Raja-Elie E. , Dalli Jesmond , Colby Jennifer K. , Krishnamoorthy Nandini , Timmons Jack Y. , Tan Sook Hwa , Colas Romain A. , Petasis Nicos A. , Serhan Charles N. , Levy Bruce D.
Published: November 2014

Significance

Neutrophil accumulation is fundamental to acute inflammation. In response to tissue injury, circulating neutrophil–platelet aggregates (N-PAs) form for secondary capture. Counterregulation of acute inflammatory processes by specialized proresolving mediators is essential to mitigate collateral injury to healthy bystander tissue. Here, we identified a biosynthetic route in human platelets for the proresolving mediator maresin 1 (MaR1) that is amplified during platelet–neutrophil interactions. In a self-resolving murine model of acute lung injury, N-PAs rapidly formed and a MaR1 counterregulatory circuit was engaged to restrain N-PAs and acute inflammation and restore homeostasis of the injured lung.
Cerebral small vessel disease-related protease HtrA1 processes latent TGF-β binding protein 1 and facilitates TGF-β signaling
Authors: Beaufort Nathalie , Scharrer Eva , Kremmer Elisabeth , Lux Vanda , Ehrmann Michael , Huber Robert , Houlden Henry , Werring David , Haffner Christof , Dichgans Martin
Published: November 2014

Significance

Cerebral small vessel disease (SVD) is a major cause of stroke and dementia. Hereditary forms, such as cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL), may provide insights into key molecular mechanisms and pathways. The serine protease HtrA1, whose activity is impaired in CARASIL, has been proposed to attenuate TGF-β signaling leading to increased pathway activity in diseased arteries. We analyzed HtrA1-deficient mouse brain tissue and mouse and CARASIL patient fibroblasts and found a reduction in signaling activity on various pathway levels suggesting a facilitating role of HtrA1. Moreover, we identified LTBP-1 as a novel HtrA1 substrate and provide evidence for its functional modulation by HtrA1-dependent proteolysis. Our data suggest down-regulation of TGF-β signaling as a key mechanism underlying CARASIL pathogenesis.
Ethnic identity as stigma in life experiences of different generations: the case of Belarusian and Ukrainian minorities in Poland
Authors: Matysiak Ilona
Published: November 2014

The main research problem addressed in this article is the pattern of reacting to stigma based on ethnic origin expressed by the representatives of different generations of Belarusian and Ukrainian minorities in Poland living under different political and ideological conditions before and after 1989. This paper is based on a qualitative empirical study that comprised 22 in-depth biographical interviews with representatives of Belarusian and Ukrainian minorities, who varied in age. The research found that while the elderly see their minority identity in terms of danger or threat, the middle generation perceives it as an obstacle in fulfilling their life aspirations in a society fully dominated by the Polish majority. The youngest interviewees seem to be the most willing to perceive their minority characteristics positively in terms of uniqueness as well as particular competences, especially bilingualism, which may give them an advantage in the labor market.
Representing minorities in the city. Education policies and minority incorporation in the capital cities of Estonia and Latvia†
Authors: Cianetti Licia
Published: November 2014

This article explores the relationship between minority city-level and state-level political representations through the analysis of the contested implementation of state education policies in Tallinn and Riga. Referring to the US debate on this issue, the article asks what role minority incorporation into city-level power structures can play for its substantive representation. The comparison between Tallinn and Riga reveals two potential answers to this question. The case of Riga illustrates how city-level representation can be an alternative representativechannelthrough which the minority can put pressure on state government and magnify its political voice within the country's democratic space. On the contrary, the case of Tallinn illustrates how a municipality can be an alternativelocusof representation, which does not guarantee minority empowerment but rather entraps the minority at the local level within the implicit understanding that the minority (or at least the parties that get the minority vote) can “have its share” locally, but it cannot hope to influence state policies. The comparison between the two cases reveals different levels of legitimacy of the minority's voice in the democratic debate of Estonia and Latvia, and shows the risks and opportunities linked to the two models of minority city-level incorporation.
JAMSS: proteomics mass spectrometry simulation in Java
Authors: Smith Rob , Prince John T.
Published: November 2014

Summary: Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of confidence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility.

Availability and implementation: The simulator creates mzML 1.1.0. It is open source software licensed under the GPLv3. The software and source are available at https://github.com/optimusmoose/JAMSS.

Contact:  2robsmith@gmail.com
Melon necrotic spot virus Replication Occurs in Association with Altered Mitochondria
Authors: Gómez-Aix Cristina , García-García María , Aranda Miguel A. , Sánchez-Pina María Amelia
Published: November 2014

Melon necrotic spot virus (MNSV) (genus Carmovirus, family Tombusviridae) is a single-stranded, positive-sense RNA virus that has become an experimental model for the analysis of cell-to-cell virus movement and translation of uncapped viral RNAs, whereas little is known about its replication. Analysis of the cytopathology after MNSV infection showed the specific presence of modified organelles that resemble mitochondria. Immunolocalization of the glycine decarboxylase complex (GDC) P protein in these organelles confirmed their mitochondrial origin. In situ hybridization and immunolocalization experiments showed the specific localization of positive-sense viral RNA, capsid protein (CP), and double-stranded (ds)RNA in these organelles meaning that replication of the virus takes place in association with them. The three-dimensional reconstructions of the altered mitochondria showed the presence of large, interconnected, internal dilations which appeared to be linked to the outside cytoplasmic environment through pores and/or complex structures, and with lipid bodies. Transient expression of MNSV p29 revealed that its specific target is mitochondria. Our data document the extensive reorganization of host mitochondria induced by MNSV, which provides a protected environment to viral replication, and show that the MNSV p29 protein is the primary determinant of this effect in the host.
Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis
Authors: Burkhardt Alyssa , Buchanan Alex , Cumbie Jason S. , Savory Elizabeth A. , Chang Jeff H. , Day Brad
Published: November 2014

Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes.
Field Response of Cucurbit Hosts toPseudoperonospora cubensisin Michigan
Authors: Cespedes-Sanchez M. C. , Naegele R. P. , Kousik C. S. , Hausbeck M. K.
Published: November 2014

Downy mildew, caused by Pseudoperonospora cubensis, is a severe foliar disease of many cucurbit crops worldwide. Forty-one cucurbit cultigens (commercial cultivars and plant introductions) from five genera (Cucumis, Citrullus, Cucurbita, Lagenaria, and Luffa) were assessed for susceptibility to P. cubensis in a research field exposed to natural inoculum in Michigan. Eight cultigens from a differential set for pathotype determination were included within the 41 cultigens to detect changes in dominant P. cubensis pathotypes present. No pathotype differences were found between 2010 and 2011. Cucumis melo cultigen MR-1 was less susceptible to Michigan P. cubensis populations than other C. melo cultigens. No symptoms or signs of infection were detected on cultigens of Cucurbita moschata and C. pepo. Disease onset was later in 2011 than 2010; greater than 90% disease severity in pickling cucumber ‘Vlaspik’ was observed in both years. This study confirmed that Cucumis is the most susceptible cucurbit genus, while Citrullus and Cucurbita cultigens were the least susceptible genera to populations of P. cubensis in Michigan. Area under the disease progress curve values indicated that disease progress was limited on all Citrullus cultigens compared with Cucumis cultigens, and pathogen sporulation was not detected under field conditions. Future studies should evaluate the ability of a reduced fungicide program to control downy mildew on less susceptible Cucumis melo ‘Edisto 47’, ‘Primo’, ‘Athena’, ‘Strike’, ‘Ananas’, ‘Banana’, and ‘Tam-Dew’. Many of the melon cultivars evaluated were selected on the basis of reported resistance to downy mildew, yet they showed significant disease symptoms. It is important to evaluate candidate cultigens for resistance to local P. cubensis populations.
Characterization of Fusarium Strains Recovered From Wheat With Symptoms of Head Blight in Kentucky
Authors: Bec S. , Ward T. , Farman M. , O’Donnell K. , Hershman D. , Van Sanford D. , Vaillancourt L. J.
Published: November 2014

Fusarium graminearum species complex (FGSC) members cause Fusarium head blight (FHB) of wheat (Triticum aestivum L.) and small grains in the United States. The U.S. population is diverse and includes several genetically distinct local emergent subpopulations, some more aggressive and toxigenic than the majority population. Kentucky is a transition zone between the Mid-Atlantic and Midwestern wheat production areas. Sixty-eight Fusarium strains were isolated from symptomatic wheat heads from central and western Kentucky and southern Indiana in 2007. A multilocus genotyping assay and a variety of additional molecular markers, including some novel markers developed using the F. graminearum genome sequence, were used to characterize the pathogen population. Five of the isolates were identified as members of two non-FGSC species, F. acuminatum and F. cf. reticulatum, but they did not cause symptoms in greenhouse tests. All the FGSC isolates belonged to the 15-ADON chemotype of F. graminearum. Comparative genetic analysis using variable nuclear tandem repeat (VNTR) markers indicated that the population in Kentucky and Indiana belonged to the dominant North American population, with some diversification likely due to local evolution. Telomere and RFLP fingerprinting markers based on repetitive sequences revealed a high degree of genetic diversity within the population, with unique genotypes found at each location, and multiple genotypes isolated from the same head.
First Report of Phakopsora pachyrhizi Causing Rust on Soybean in Malawi
Authors: Murithi H. M. , Beed F. D. , Soko M. M. , Haudenshield J. S. , Hartman G. L.
Published: November 2014

Soybean rust (SBR), caused by Phakopsora pachyrhizi, has become established in Africa since the first report in Uganda in 1996 (2). The urediniospores, as windborne propagules, have infested new regions of Africa, initiating SBR in many countries, including Ghana and Democratic Republic of the Congo in 2007 (4) and Tanzania in 2014 (3). No refereed reports have been published about rust in Malawi, but some people have indicated that soybean rust may have been observed as early as 2008. Typical symptoms and signs of SBR, including leaf yellowing and tan, sporulating uredinia, were observed on soybean in May 2014 during field surveys in the major soybean-growing areas of Malawi, including the central (Dowa, Mchinji, and Kasungu) and southern (Thyolo) regions in nine out of 12 sites surveyed. When microscopically examined, urediniospores were elliptical, echinulate, and hyaline to pale yellowish brown. Leaves exhibiting sporuliferous uredinia were sent by APHIS permit to the University of Illinois. To confirm the pathogen, symptomatic soybean leaf tissue of approximately 1 cm2 was excised from each of the samples, and DNA was extracted using the FastDNA Spin Kit (MP Biomedicals, Solon, OH), with further purification using the MicroElute DNA Clean-up Kit (Omega Bio-Tek, Norcross, GA). The resulting DNA was analyzed by quantitative PCR using published Taqman assays for P. pachyrhizi and P. meibomiae, with a multiplexed exogenous internal control reaction to validate negative results (1). P. pachyrhizi DNA was detected in excess of 180,000 genome equivalents/cm2 in all samples, indicating a substantial infection. P. meibomiae DNA was determined to be absent from all samples, within the limit of quantification of ~2 pg DNA/cm2. Urediniospores dislodged from three leaves and inoculated onto susceptible soybean cultivar Williams 82 produced tan lesions after 2 weeks of incubation in a detached-leaf assay. This is the first confirmed report of P. pachyrhizi causing rust on soybean in Malawi, putting at risk 14,000 ha currently under soybean production. The reports of soybean rust in Malawi and adjoining countries will alter soybean production practices and research interests. In some cases, foliar application of fungicides has increased and planting dates have been changed to avoid conditions that are most conducive for rust development. Efforts to understand the virulence and genetic diversity of the pathogen in the region are needed in order to develop and deploy resistant cultivars.

References: (1) J. S. Haudenshield and G. L. Hartman. Plant Dis. 95:343, 2011. (2) R. Kawuki, et al. Afr. Crop Sci. J. 11:301, 2003. (3) H. M. Murithi et al. Plant Dis. 98:1586, 2014. (4) P. S. Ojiambo et al. Plant Dis. 91:1204, 2007.
Effectiveness of 14 Fungicides for Suppressing Lesions Caused by Phytophthora capsici on Inoculated Stems of Chile Pepper Seedlings
Authors: Matheron Michael E. , Porchas Martin
Published: November 2014

Phytophthora blight, caused by the oomycete pathogen Phytophthora capsici, is an economically important disease in bell and chile pepper. Fourteen different fungicides were evaluated with respect to inhibition of stem lesion growth on chile pepper seedlings inoculated with mycelium or with zoospores of P. capsici 1 or 3 weeks after treatment of plant foliage and stems or roots. Fungicides containing ametoctradin + dimethomorph and fluopicolide were the most effective among tested products in both experiments across eight trial parameters (inoculum type, inoculation time after treatment, and fungicide application site). Other active ingredients, including acibenzolar-S-methyl, dimethomorph, fenamidone, ethaboxam, mandipropamid, mefenoxam, and oxathiapiprolin, were most effective in reducing stem lesion growth in three to seven of the eight trial parameters evaluated. Compared to nontreated plants, stem lesion inhibition ranged from 84.1 to 100%. Data from these trials demonstrate the comparative effectiveness of tested products under controlled environmental conditions favorable for disease development; however, confirmation of these findings is required in field trials, where plant and environmental conditions will be variable.

Accepted for publication 18 September 2014. Published 1 November 2014.
Effects of Ultraprotective Ventilation, Extracorporeal Carbon Dioxide Removal, and Spontaneous Breathing on Lung Morphofunction and Inflammation in Experimental Severe Acute Respiratory Distress Syndrome
Authors: Güldner Andreas , Kiss Thomas , Bluth Thomas , Uhlig Christopher , Braune Anja , Carvalho Nadja , Quast Theresa , Rentzsch Ines , Huhle Robert , Spieth Peter , Richter Torsten , Saddy Felipe , Rocco Patricia R. M. , Kasper Michael , Koch Thea , Pelosi Paolo , de Abreu Marcelo Gama
Published: November 2014

AbstractAbstract

In a model of severe acute respiratory distress syndrome in pigs, mechanical ventilation with 3 ml/kg tidal volume and extracorporeal carbon dioxide removal without spontaneous breathing slightly reduced lung histologic damage. Spontaneous breathing during ultraprotective ventilation improved gas exchange and distribution of ventilation, but pressure support increased lung inflammation.

Background:

To investigate the role of ultraprotective mechanical ventilation (UP-MV) and extracorporeal carbon dioxide removal with and without spontaneous breathing (SB) to improve respiratory function and lung protection in experimental severe acute respiratory distress syndrome.

Methods:

Severe acute respiratory distress syndrome was induced by saline lung lavage and mechanical ventilation (MV) with higher tidal volume (VT) in 28 anesthetized pigs (32.8 to 52.5 kg). Animals (n = 7 per group) were randomly assigned to 6 h of MV (airway pressure release ventilation) with: (1) conventional P-MV with VT ≈6 ml/kg (P-MVcontr); (2) UP-MV with VT ≈3 ml/kg (UP-MVcontr); (3) UP-MV with VT ≈3 ml/kg and SB (UP-MVspont); and (4) UP-MV with VT ≈3 ml/kg and pressure supported SB (UP-MVPS). In UP-MV groups, extracorporeal carbon dioxide removal was used.

Results:

The authors found that: (1) UP-MVcontr reduced diffuse alveolar damage score in dorsal lung zones (median[interquartile]) (12.0 [7.0 to 16.8] vs. 22.5 [13.8 to 40.8]), but worsened oxygenation and intrapulmonary shunt, compared to P-MVcontr; (2) UP-MVspont and UP-MVPS improved oxygenation and intrapulmonary shunt, and redistributed ventilation towards dorsal areas, as compared to UP-MVcontr; (3) compared to P-MVcontr, UP-MVcontr and UP-MVspont, UP-MVPS yielded higher levels of tumor necrosis factor-α (6.9 [6.5 to 10.1] vs. 2.8 [2.2 to 3.0], 3.6 [3.0 to 4.7] and 4.0 [2.8 to 4.4] pg/mg, respectively) and interleukin-8 (216.8 [113.5 to 343.5] vs. 59.8 [45.3 to 66.7], 37.6 [18.8 to 52.0], and 59.5 [36.1 to 79.7] pg/mg, respectively) in dorsal lung zones.

Conclusions:

In this model of severe acute respiratory distress syndrome, MV with VT ≈3 ml/kg and extracorporeal carbon dioxide removal without SB slightly reduced lung histologic damage, but not inflammation, as compared to MV with VT = 4 to 6 ml/kg. During UP-MV, pressure supported SB increased lung inflammation.
Intracranial Extension of an Orbital Epidermoid Cyst
Authors: Burnham Jordan M. , Lewis Kyle
Published: November 2014

Epidermoid and dermoid cysts represent the most common cystic lesions of the orbit and commonly arise from bony sutures or the intradiplpoic space of orbital bones. Massive intracranial extension of an epidermoid cyst arising from the intradiploic space of an orbital bone is very rarely seen. We present a case of a 55-year-old male who was incidentally found to have massive intracranial extension of an intradiploic epidermoid cyst of the superolateral orbital bone with minimal symptoms. The cyst was completely excised via a pterional craniotomy and lateral orbitotomy by neurosurgery and oculoplastic surgery teams. The patient suffered no complications and is doing very well.
Fibrous Hamartoma of Infancy in the Eyelid: A Rare Presentation
Authors: Tran Ann Q. , Thuro Bradley A. , Albert Daniel M. , Lucarelli Mark J. , Potter Heather D.
Published: November 2014

A 6-year-old girl presented with a left nodular mass around the punctum. Previous debulking in a similar location at 10 weeks and 8 months of age confirmed fibrous hamartoma of infancy. Pathology at the initial surgery revealed benign-appearing fibroadipose tissue, vasculature, and smooth muscle. Pathologic examination from the third debulking illustrated less fibrous trabeculae extending into increased amounts of mature-appearing adipocytes with collections of immature-appearing fibrocytes. The lesion had slight differences in pathology compared with prior surgical specimens; however, was still consistent with fibrous hamartoma of infancy. No recurrence has been reported since the last surgery.
Faecal Calprotectin in Suspected Paediatric Inflammatory Bowel Disease
Authors: Degraeuwe Pieter L.J. , Beld Monique P.A. , Ashorn Merja , Canani Roberto Berni , Day Andrew S. , Diamanti Antonella , Fagerberg Ulrika L. , Henderson Paul , Kolho Kaija‐Leena , Van de Vijver Els , van Rheenen Patrick F. , Wilson David C. , Kessels Alfons G.H.
Published: November 2014

Objectives:

The diagnostic accuracy of faecal calprotectin (FC) concentration for paediatric inflammatory bowel disease (IBD) is well described at the population level, but not at the individual level. We reassessed the diagnostic accuracy of FC in children with suspected IBD and developed an individual risk prediction rule using individual patient data.

Methods:

MEDLINE, EMBASE, DARE, and MEDION databases were searched to identify cohort studies evaluating the diagnostic performance of FC in paediatric patients suspected of having IBD. A standard study‐level meta‐analysis was performed. In an individual patient data meta‐analysis, we reanalysed the diagnostic accuracy on a merged patient dataset. Using logistic regression analysis we investigated whether and how the FC value and patient characteristics influence the diagnostic precision. A prediction rule was derived for use in clinical practice and implemented in a spreadsheet calculator.

Results:

According to the study‐level meta‐analysis (9 studies, describing 853 patients), FC has a high overall sensitivity of 0.97 (95% confidence interval [CI] 0.92–0.99) and a specificity of 0.70 (0.59–0.79) for diagnosing IBD. In the patient‐level pooled analysis of 742 patients from 8 diagnostic accuracy studies, we calculated that at an FC cutoff level of 50 μg/g there would be 17% (95% CI 15–20) false‐positive and 2% (1–3) false‐negative results. The final logistic regression model was based on individual data of 545 patients and included both FC level and age. The area under the receiver operating characteristic curve of this derived prediction model was 0.92 (95% CI 0.89–0.94).

Conclusions:

In high‐prevalence circumstances, FC can be used as a noninvasive biomarker of paediatric IBD with only a small risk of missing cases. To quantify the individual patients' risk, we developed a simple prediction model based on FC concentration and age. Although the derived prediction rule cannot substitute the clinical diagnostic process, it can help in selecting patients for endoscopic evaluation.
Gastrointestinal Manifestations in Diploid/Triploid Mixoploidy
Authors: Lalani Farida K. , Elsner Garrett L. , Lebel Robert Roger , Beg Mirza B.
Published: November 2014

A girl infant was delivered by cesarean section at 32 weeks of gestation because of growth arrest and poor movement patterns. The infant had feeding problems, which were based on gastroesophageal reflux, laryngomalacia, and decreased gut motility. Hypotonia was notable from the outset, and the patient eventually displayed significant delays in both motor and cognitive milestones. Meanwhile, lymphocytes had yielded a normal karyotype (46,XX), but at 2 years of age the patient underwent a skin biopsy and mosaicism because a 68,XX cell line was discovered in fibroblasts. At the age 6.4 years, the patient is short of stature below the 3rd percentile but has a weight at the 42nd percentile and head circumference above the 97th percentile. Other phenotypic features include low‐set ears, piebald irides and scalp hair, eyelid ptosis, strabismus, broad nasal bridge, anteverted nares, upswept eyebrows, hypoplastic teeth, pectus excavatum, hypoplastic labia, scoliosis, 3–4 finger syndactyly, and 2–3 toe syndactyly. We present this case with a review of the literature for mixoploidy (the rare event of mosaicism for diploid and triploid cell lines). We add to the existing data on the clinical features of diploid/triploid mixoploidy. The complexities of the gastrointestinal problems make this case unusual.
Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains
Authors: Ross Robert J.H. , Yates C.A. , Baker R.E.
Published: November 2014

A key feature of cell migration is how cell movement is affected by cell-cell interactions. Furthermore, many cell migratory processes such as neural crest stem cell migration [1, 2] occur on growing domains or in the presence of a chemoattractant. Therefore, it is important to study interactions between migrating cells in the context of domain growth and directed motility. Here we compare discrete and continuum models describing the spatial and temporal evolution of a cell population for different types of cell-cell interactions on static and growing domains. We suggest that cell-cell interactions can be inferred from population density characteristics in the presence of motility bias, and these population density characteristics for different cell-cell interactions are conserved on both static and growing domains. We also study the expected displacement of a tagged cell, and show that different types of cell-cell interactions can give rise to cell trajectories with different characteristics. These characteristics are conserved in the presence of domain growth, however, they are diminished in the presence of motility bias. Our results are relevant for researchers who study the existence and role of cell-cell interactions in biological systems, so far as we suggest that different types of cell-cell interactions could be identified from cell density and trajectory data.
Single haplotype assembly of the human genome from a hydatidiform mole
Authors: Steinberg Karyn Meltz , Schneider Valerie A. , Graves-Lindsay Tina A. , Fulton Robert S. , Agarwala Richa , Huddleston John , Shiryev Sergey A. , Morgulis Aleksandr , Surti Urvashi , Warren Wesley C. , Church Deanna M. , Eichler Evan E. , Wilson Richard K.
Published: November 2014

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly.
Involvement of the Electrophilic Isothiocyanate Sulforaphane in Arabidopsis Local Defense Responses
Authors: Andersson Mats X. , Nilsson Anders K. , Johansson Oskar N. , Boztaş Gülin , Adolfsson Lisa E. , Pinosa Francesco , Petit Christel Garcia , Aronsson Henrik , Mackey David , Tör Mahmut , Hamberg Mats , Ellerström Mats
Published: November 2014

Plants defend themselves against microbial pathogens through a range of highly sophisticated and integrated molecular systems. Recognition of pathogen-secreted effector proteins often triggers the hypersensitive response (HR), a complex multicellular defense reaction where programmed cell death of cells surrounding the primary site of infection is a prominent feature. Even though the HR was described almost a century ago, cell-to-cell factors acting at the local level generating the full defense reaction have remained obscure. In this study, we sought to identify diffusible molecules produced during the HR that could induce cell death in naive tissue. We found that 4-methylsulfinylbutyl isothiocyanate (sulforaphane) is released by Arabidopsis (Arabidopsis thaliana) leaf tissue undergoing the HR and that this compound induces cell death as well as primes defense in naive tissue. Two different mutants impaired in the pathogen-induced accumulation of sulforaphane displayed attenuated programmed cell death upon bacterial and oomycete effector recognition as well as decreased resistance to several isolates of the plant pathogen Hyaloperonospora arabidopsidis. Treatment with sulforaphane provided protection against a virulent H. arabidopsidis isolate. Glucosinolate breakdown products are recognized as antifeeding compounds toward insects and recently also as intracellular signaling and bacteriostatic molecules in Arabidopsis. The data presented here indicate that these compounds also trigger local defense responses in Arabidopsis tissue.
Brassinosteroid Regulates Cell Elongation by Modulating Gibberellin Metabolism in Rice
Authors: Tong Hongning , Xiao Yunhua , Liu Dapu , Gao Shaopei , Liu Linchuan , Yin Yanhai , Jin Yun , Qian Qian , Chu Chengcai
Published: November 2014

Brassinosteroid (BR) and gibberellin (GA) are two predominant hormones regulating plant cell elongation. A defect in either of these leads to reduced plant growth and dwarfism. However, their relationship remains unknown in rice (Oryza sativa). Here, we demonstrated that BR regulates cell elongation by modulating GA metabolism in rice. Under physiological conditions, BR promotes GA accumulation by regulating the expression of GA metabolic genes to stimulate cell elongation. BR greatly induces the expression of D18/GA3ox-2, one of the GA biosynthetic genes, leading to increased GA1 levels, the bioactive GA in rice seedlings. Consequently, both d18 and loss-of-function GA-signaling mutants have decreased BR sensitivity. When excessive active BR is applied, the hormone mostly induces GA inactivation through upregulation of the GA inactivation gene GA2ox-3 and also represses BR biosynthesis, resulting in decreased hormone levels and growth inhibition. As a feedback mechanism, GA extensively inhibits BR biosynthesis and the BR response. GA treatment decreases the enlarged leaf angles in plants with enhanced BR biosynthesis or signaling. Our results revealed a previously unknown mechanism underlying BR and GA crosstalk depending on tissues and hormone levels, which greatly advances our understanding of hormone actions in crop plants and appears much different from that in Arabidopsis thaliana.
4-(3-Azaniumylpropyl)morpholin-4-ium chloride hydrogen oxalate: an unusual example of a dication with different counter-anions
Authors: Traut-Johnstone Telisha , Kriel Frederik H. , Hewer Raymond , Williams D. Bradley G.
Published: November 2014

The mixed organic–inorganic title salt, C7H18N2O2+·C2HO4−·Cl−, forms an assembly of ionic components which are stabilized through a series of hydrogen bonds and charge-assisted intermolecular interactions. The title assembly crystallizes in the monoclinicC2/cspace group withZ= 8. The asymmetric unit consists of a 4-(3-azaniumylpropyl)morpholin-4-ium dication, a hydrogen oxalate counter-anion and an inorganic chloride counter-anion. The organic cations and anions are connected through a network of N—H...O, O—H...O and C—H...O hydrogen bonds, forming several intermolecular rings that can be described by the graph-set notationsR33(13),R21(5),R12(5),R21(6),R23(6),R22(8) andR33(9). The 4-(3-azaniumylpropyl)morpholin-4-ium dications are interconnected through N—H...O hydrogen bonds, formingC(9) chains that run diagonally along theabface. Furthermore, the hydrogen oxalate anions are interconnectedviaO—H...O hydrogen bonds, forming head-to-tailC(5) chains along the crystallographicbaxis. The two types of chains are linked through additional N—H...O and O—H...O hydrogen bonds, and the hydrogen oxalate chains are sandwiched by the 4-(3-azaniumylpropyl)morpholin-4-ium chains, forming organic layers that are separated by the chloride anions. Finally, the layered three-dimensional structure is stabilizedviaintermolecular N—H...Cl and C—H...Cl interactions.
Comparative structural analysis of 2,7-diethoxy-1,8-bis(4-phenoxybenzoyl)naphthalene and its homologues: orientation of the 4-phenoxybenzoyl groups at the 1- and 8-positions of the naphthalene ring
Authors: Yoshiwaka Sayaka , Sasagawa Kosuke , Noguchi Keiichi , Yonezawa Noriyuki , Okamoto Akiko
Published: November 2014

The title molecule, C40H32O6, possesses crystallographically imposed twofold symmetry, with the central two C atoms of the naphthalene unit sited on the rotation axis. The two 4-phenoxybenzoyl groups in the molecule are twisted away from the attached naphthalene unit, with a torsion angle of 66.76 (15)° between the naphthalene unit and the carbonyl group (C—C—C=O), and are oriented in mutually opposing directions (antiorientation). There is an apparent difference in the conformations of the 4-phenoxybenzoyl groups at the 1- and 8-positions of the naphthalene ring between the title molecule and its methoxy-bearing homologue [Hijikataet al.(2010).Acta Cryst.E66, o2902–o2903]. Whilst the 4-phenoxybenzoyl groups in 2,7-diisopropoxy-1,8-bis(4-phenoxybenzoyl)naphthalene [Yoshiwakaet al.(2013).Acta Cryst.E69, o242] are situated in the sameantiorientation as the title molecule, those of 2,7-dimethoxy-1,8-bis(4-phenoxybenzoyl)naphthalene are oriented in the same direction with respect to the naphthalene ring system,i.e.in asynorientation.
A twofold interpenetrating three-dimensional CdIIcoordination framework: poly[[μ2-1,3-bis(2-methyl-1H-imidazol-1-yl)benzene](μ3-5-nitrobenzene-1,3-dicarboxylato)cadmium(II)]
Authors: Li Le , Tao Jian-Qing
Published: November 2014

A twofold interpenetrating three-dimensional CdIIcoordination framework, [Cd(C8H3NO6)(C14H14N4)]n, has been prepared and characterized by IR spectroscopy, elemental analysis, thermal analysis and single-crystal X-ray diffraction. The asymmetric unit consists of a divalent CdIIatom, one 1,3-bis(2-methyl-1H-imidazol-1-yl)benzene (1,3-BMIB) ligand and one fully deprotonated 5-nitrobenzene-1,3-dicarboxylate (NO2-BDC2−) ligand. The coordination sphere of the CdIIatom consists of five O-donor atoms from three different NO2-BDC2−ligands and two imidazole N-donor atoms from two different 1,3-BMIB ligands, forming a distorted {CdN2O5} pentagonal bipyramid. The NO2-BDC ligand links three CdIIatomsviaa μ1-η1:η1chelating mode and a μ2-η2:η1bridging mode. The title compound is a twofold interpenetrating 3,5-connected network with the {42.65.83}{42.6} topology. In addition, the compound exhibits fluorescence emissions in the solid state at room temperature.