bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhinosporidiosis of the upper airways and trachea
Authors: Madana J , Yolmo D , Gopalakrishnan S , Saxena S Kumar 
Published: June 2010

AbstractObjective:We report an extremely rare case of rhinosporidiosis with involvement of both larynx and trachea, together with coexisting nasal, nasopharyngeal and oropharyngeal lesions, in a 32-year-old man.Method:Case report and review of the world literature concerning laryngotracheal and disseminated rhinosporidiosis.Results:A 32-year-old, South Indian man presented with a nasal mass of four years' duration, with progressive hoarseness for one year. Strawberry-like rhinosporidial masses were seen in both nasal cavities. Fibre-optic laryngoscopic examination revealed reddish masses with whitish surface specks, involving the glottis, subglottis and trachea. Computed tomography revealed soft tissue opacities involving both nasal cavities and the nasopharynx and extending to the oropharynx, with involvement of the larynx and trachea. Direct laryngoscopy and rigid bronchoscopy guided excision of the laryngeal and tracheal lesions was performed.Conclusion:Rhinosporidiosis is a chronic, granulomatous disease which usually affects the mucous membranes of the nose and nasopharynx. Lower dissemination into the trachea is extremely rare. Laryngotracheal involvement poses many diagnostic and therapeutic challenges, due to the potential risk of bleeding and aspiration. In the presented case, local spread of rhinosporidiosis, due to direct spillage of spores from the nasopharynx into the larynx during episodes of bleeding or previous surgery, may have resulted in laryngotracheal involvement, although systemic spread cannot be excluded.
Tumefactive fibroinflammatory lesion of the frontal sinus
Authors: Philpott C M , Javer A R 
Published: June 2010

AbstractObjective:A 65-year-old man presented with a nine-month history of swelling in the midline of the forehead. After surgical intervention, this lesion was found to be a tumefactive fibroinflammatory lesion of the frontal sinus. This case report and review aims to report this new location for tumefactive fibroinflammatory lesion, and to discuss whether, in retrospect, there would have been alternative options to surgery.Methods:Case report and literature review.Results:Tumefactive fibroinflammatory lesions are rare. Although cases in the sinonasal tract have been described, none involving the frontal sinus have previously been reported. A review of the literature suggests that these lesions have an association with other fibroinflammatory lesions, and may be amenable to systemic steroid therapy.Conclusion:Each case should be managed on its merits, and a biopsy taken followed by subsequent screening for associated fibroinflammatory lesions. In the case of an isolated lesion, a surgical approach is probably favoured in a patient suitable for general anaesthesia.
Radiological observations on the olfactory fossa and ethmoid roof
Authors: Elwany S , Medanni A , Eid M , Aly A , El-Daly A , Ammar S R 
Published: June 2010

AbstractObjective:To establish normative dimensions for the depth of the olfactory fossa, the length and angulation of the lateral lamella of the cribriform plate, and the height of the ethmoid roof, in adult males and females.Design:The study assessed 300 high resolution, multislice computed tomography scans of the paranasal sinuses, which were evaluated using Merge Efilm software (version 2.0.0, build 37).Results:According to the original Keros classification, the type II olfactory fossa was the commonest type in men (66.7 per cent), while the type I fossa was commonest in women (53 per cent). A difference of 3 mm or more between the depths of the right and left olfactory fossae was present in 11 per cent of men and 2 per cent of women. The lateral lamella of the cribriform plate was significantly shorter and less oblique in men than in women. The length of the lateral lamella was greater anteriorly than posteriorly in both sexes. There was a statistically significant difference between the angle of the lateral lamellae, comparing right and left sides. The ethmoid roof was lower in women than men.Conclusion:The observed differences between men and women and between the right and left sides are of surgical importance, and should alert surgeons to the need for thorough, systematic pre-operative evaluation of computed tomography scans.
Breakfast skipping and its relation to BMI and health-compromising behaviours among Greek adolescents
Authors: Kapantais Efthymios , Chala Eftychia , Kaklamanou Daphne , Lanaras Leonidas , Kaklamanou Myrto , Tzotzas Themistoklis 
Published: June 2010

AbstractObjectiveThe increasing prevalence of obesity worldwide is a major health concern. Our study, which is part of the First National Epidemiological Study of Obesity in Greece, aimed to assess (i) breakfast habits and their relationship to BMI in Greek adolescents, as well as (ii) breakfast skipping in relation to other health behaviours.DesignEpidemiological survey throughout Greece. Participants completed a questionnaire concerning breakfast habits and many lifestyle parameters.SettingThe survey was conducted in schools throughout Greece.SubjectsAnthropometric measurements were performed on 6500 boys and 7778 girls, aged 13–19 years, from schools throughout Greece.ResultsAmong both boys and girls, breakfast consumers had a lower BMI than breakfast skippers. Moreover, breakfast skippers among both boys and girls were found to smoke more than breakfast consumers. The proportion of boys and girls who ate breakfast was found to be greater among those who had never been on a diet than among those who had already experienced dieting. Leisure-time activity was greater in breakfast consumers than breakfast skippers; among boys, 71·8 % of breakfast consumers walked compared with 66·4 % of breakfast skippers, whereas 38·4 % and 35·0 %, respectively, exercised. Among girls, these percentages were 73·1 %v.68·7 % for walking and 36·7 %v.31·5 % for exercising.ConclusionsWe found that breakfast skipping can be part of a constellation of several unhealthy lifestyle parameters and is related to higher BMI in Greek adolescents.
A fluorophore ligase for site-specific protein labeling inside living cells
Authors: Uttamapinant Chayasith , White Katharine A. , Baruah Hemanta , Thompson Samuel , Fernández-Suárez Marta , Puthenveetil Sujiet , Ting Alice Y. 
Published: June 2010

Biological microscopy would benefit from smaller alternatives to green fluorescent protein for imaging specific proteins in living cells. Here we introduce PRIME (PRobe Incorporation Mediated by Enzymes), a method for fluorescent labeling of peptide-fused recombinant proteins in living cells with high specificity. PRIME uses an engineered fluorophore ligase, which is derived from the natural
Escherichia coli
enzyme lipoic acid ligase (LplA). Through structure-guided mutagenesis, we created a mutant ligase capable of recognizing a 7-hydroxycoumarin substrate and catalyzing its covalent conjugation to a transposable 13-amino acid peptide called LAP (LplA Acceptor Peptide). We showed that this fluorophore ligation occurs in cells in 10 min and that it is highly specific for LAP fusion proteins over all endogenous mammalian proteins. By genetically targeting the PRIME ligase to specific subcellular compartments, we were able to selectively label spatially distinct subsets of proteins, such as the surface pool of neurexin and the nuclear pool of actin.
Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy
Authors: Jiang Huaidong , Song Changyong , Chen Chien-Chun , Xu Rui , Raines Kevin S. , Fahimian Benjamin P. , Lu Chien-Hung , Lee Ting-Kuo , Nakashima Akio , Urano Jun , Ishikawa Tetsuya , Tamanoi Fuyuhiko , Miao Jianwei 
Published: June 2010

Microscopy has greatly advanced our understanding of biology. Although significant progress has recently been made in optical microscopy to break the diffraction-limit barrier, reliance of such techniques on fluorescent labeling technologies prohibits quantitative 3D imaging of the entire contents of cells. Cryoelectron microscopy can image pleomorphic structures at a resolution of 3–5 nm, but is only applicable to thin or sectioned specimens. Here, we report quantitative 3D imaging of a whole, unstained cell at a resolution of 50–60 nm by X-ray diffraction microscopy. We identified the 3D morphology and structure of cellular organelles including cell wall, vacuole, endoplasmic reticulum, mitochondria, granules, nucleus, and nucleolus inside a yeast spore cell. Furthermore, we observed a 3D structure protruding from the reconstructed yeast spore, suggesting the spore germination process. Using cryogenic technologies, a 3D resolution of 5–10 nm should be achievable by X-ray diffraction microscopy. This work hence paves a way for quantitative 3D imaging of a wide range of biological specimens at nanometer-scale resolutions that are too thick for electron microscopy.
Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the
Drosophila
RNA polymerase II transcription elongation complex
Authors: Missra Anamika , Gilmour David S. 
Published: June 2010

Negative elongation factor (NELF) and 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole sensitivity-inducing factor (DSIF) are involved in pausing RNA Polymerase II (Pol II) in the promoter-proximal region of the
hsp
70 gene in
Drosophila
, before heat shock induction. Such blocks in elongation are widespread in the
Drosophila
genome. However, the mechanism by which DSIF and NELF participate in setting up the paused Pol II remains unclear. We analyzed the interactions among DSIF, NELF, and a reconstituted
Drosophila
Pol II elongation complex to gain insight into the mechanism of pausing. Our results show that DSIF and NELF require a nascent transcript longer than 18 nt to stably associate with the Pol II elongation complex. Protein-RNA cross-linking reveals that Spt5, the largest subunit of DSIF, contacts the nascent RNA as the RNA emerges from the elongation complex. Taken together, these results provide a possible model by which DSIF binds the elongation complex via association with the nascent transcript and subsequently recruits NELF. Although DSIF and NELF were both required for inhibition of transcription, we did not detect a NELF-RNA contact when the nascent transcript was between 22 and 31 nt long, which encompasses the region where promoter-proximal pausing occurs on many genes in
Drosophila
. This raises the possibility that RNA binding by NELF is not necessary in promoter-proximal pausing.
Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences
Authors: Tzul Franco O. , Bowler Bruce E. 
Published: June 2010

How the primary sequence of a protein encodes conformational preferences that operate early in folding to promote efficient formation of the correct native topology is still poorly understood. To address this issue, we have prepared a set of yeast iso-1-cytochrome
c
variants that contain polyalanine inserts ranging from 6 to 30 residues in length near the N terminus of the protein. We study the thermodynamics and kinetics of His-heme loop formation in the denatured state at 3 and 6 M guanidine-HCl concentration. We find that polyalanine closely approximates a random coil with excluded volume giving scaling exponents,
ν
3
, for equilibrium loop formation of 2.26 ± 0.13 and 1.97 ± 0.04 in 3 and 6 M guanidine-HCl, respectively. The rate of loop breakage initially decreases and then becomes independent of loop size as would be expected for a random coil. Comparison with previously reported data for denatured state His-heme loop formation for iso-1-cytochrome
c
and
Rhodopseudomonas palustris
cytochrome
c
′, shows that foldable sequences deviate significantly from random coil behavior and that the deviation is fold-dependent.
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
Authors: Zhao Huiying , Yang Yuedong , Zhou Yaoqi 
Published: June 2010

Abstract
Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein–DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state.
Results: We showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 non-binding proteins. The MCC value is substantially higher than the best MCC value of 0.69 given by previous methods. Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively DNA binding and only 1 protein whose annotated functions do not contain DNA binding, while the remaining proteins have unknown function. The method provides a highly accurate and sensitive technique for structure-based prediction of DNA binding proteins.
Availability: The method is implemented as a part of the Structure-based function-Prediction On-line Tools (SPOT) package available at http://sparks.informatics.iupui.edu/spot
Contact: yqzhou@iupui.edu
The effects of adding torasemide to standard therapy on peak oxygen consumption, natriuretic peptides, and quality of life in patients with compensated left ventricular systolic dysfunction
Authors: Gupta Sanjay , Waywell Carolyn , Gandhi Nandkumar , Clayton Nigel , Keevil Brian , Clark Andrew L. , Ng Leong L. , Brooks Nicholas , Neyses Ludwig 
Published: June 2010

AimsDiuretics, when used to treat congestion in patients with chronic heart failure, improve symptoms and, perhaps, prognosis but little information is available to guide their use in patients with left ventricular systolic dysfunction (LVSD) who are not congested. Chronic diuretic therapy causes persistent and potentially harmful neuroendocrine activation. Alternatively, in patients in whom neuroendocrine activation is blocked with angiotensin‐converting enzyme (ACE)‐inhibitors and β‐blockers, diuretics may be beneficial by decreasing preload and afterload and preventing congestion. We aimed to assess the effect of the loop diuretic, torasemide on quality of life, and surrogate markers of prognosis when given to patients with LVSD who were not clinically congested and who were optimally treated with ACE‐inhibitors (or angiotensin receptor antagonists) and β‐blockers.Methods and resultsThirty patients with stable LVSD who had no clinically detectable fluid overload were randomized to receive either torasemide 5 mg daily or placebo for 3 months (Phase A), and after a washout phase of 2 months, cross‐over was performed for 3 months (Phase B). Diuretic therapy did not cause significant change in peak VO2, mean N‐terminal pro‐hormone brain natriuretic peptide (NT‐proBNP) levels, or measures of quality of life compared with placebo. Diuretic therapy did however lead to significant fall in systolic and diastolic blood pressures and increase in plasma renin levels compared with placebo.ConclusionDiuretic therapy with torasemide is not superior to placebo in improving peak VO2 or reducing NT‐proBNP levels in patients with left ventricular dysfunction who are not clinically congested.
Estimating the target strength of live, free-swimming chokka squid Loligo reynaudii at 38 and 120 kHz
Authors: Soule Michael A. , Hampton Ian , Lipiński Marek R. 
Published: June 2010

AbstractSoule, M. A., Hampton, I., and Lipiński, M. R. 2010. Estimating the target strength of live, free-swimming chokka squid Loligo reynaudii at 38 and 120 kHz. – ICES Journal of Marine Science, 67: 1381–1391. Estimates of the target strength (TS) of the loliginid squid Loligo reynaudii at 120 kHz were made from ex situ experiments on 38 caged, but free-swimming animals, and at 38 and 120 kHz from 17 in situ experiments on spawning aggregations in the wild conducted from a research vessel and from small boats. The cage experiments suggested that the backscattering cross section is proportional to mantle length (ML), which would not be expected from simple considerations of ML in relation to wavelength. A similar relationship was found during the in situ experiments conducted from the research vessel. The TS estimates from the research vessel agreed well with those from the cage experiments, for both of the two methods used to extract squid TS distributions from the overall TS distributions, but were some 2–3 dB lower than those from the small boats. This suggests that in situ estimates are affected by the vessel and/or the way in which squid react to it. It is concluded that ex situ experiments on L. reynaudii TS are of most value as a complement to in situ experiments, which should be made concurrently while surveying, using systems capable of having higher volume resolution than in the current experiments, to maximize the applicability of the estimates to the survey data.
Variation in Antiherbivore Defense Responses in Synthetic Nicotiana Allopolyploids Correlates with Changes in Uniparental Patterns of Gene Expression
Authors: Anssour Samir , Baldwin Ian T. 
Published: June 2010

Abstract
We examined the expression of Nicotiana attenuata (Na) and Nicotiana obtusifolia (No) herbivore-induced genes in synthetic autopolyploids (NaT and NoT) and five independent allopolyploid Nicotiana × obtusiata (N×o) lines to understand how the expression of genes regulating complex polygenetic defense traits is altered in the early stages of allopolyploid hybridization. In Na, applying Manduca sexta oral secretions (OS) to wounds rapidly increased the transcript accumulation of wound-induced protein kinase (WIPK), lipoxygenase 3 (LOX3), nonexpressor of pathogenesis-related 1 (NPR1), and jasmonate-resistant 4 (JAR4) genes; these were correlated with increases in accumulation of jasmonic acid (JA), jasmonate-isoleucine, and trypsin protease inhibitors (TPIs). In No, OS elicitation reduced NPR1 transcripts and increased the level of salicylic acid (SA) that appeared to antagonize JA and JA-mediated defenses. OS elicited N×o lines, accumulated high levels of the uniparental transcript of WIPK, LOX3, JAR4, and TPI, but low levels of both parental NPR1 transcripts that in turn were correlated with an increase in SA and a decrease in JA levels, suggesting SA/JA antagonism in the allopolyploid crosses. Methyl jasmonate treatment of N×o lines elicited transcripts of both parental LOX3, JAR4, and TPIs, demonstrating that the uniparental pattern observed after OS elicitation was not due to gene inactivation. TPIs were induced at different levels among N×o lines; some lines expressed high levels comparable to Na, others low levels similar to No, suggesting that synthetic neoallopolyploids rapidly readjust the expression of their parental defensive genes to generate diverse antiherbivore responses. Changes in the expression of key genes and posttranscriptional events likely facilitate adaptive radiations during allopolyploid speciation events.
Myosin XI Is Essential for Tip Growth inPhyscomitrella patens
Authors: Vidali Luis , Burkart Graham M. , Augustine Robert C. , Kerdavid Erin , Tüzel Erkan , Bezanilla Magdalena 
Published: June 2010

AbstractClass XI myosins are plant specific and responsible for cytoplasmic streaming. Because of the large number of myosin XI genes in angiosperms, it has been difficult to determine their precise role, particularly with respect to tip growth. The moss Physcomitrella patens provides an ideal system to study myosin XI function. P. patens has only two myosin XI genes, and these genes encode proteins that are 94% identical to each other. To determine their role in tip growth, we used RNA interference to specifically silence each myosin XI gene using 5′ untranslated region sequences. We discovered that the two myosin XI genes are functionally redundant, since silencing of either gene does not affect growth or polarity. However, simultaneous silencing of both myosin XIs results in severely stunted plants composed of small rounded cells. Although similar to the phenotype resulting from silencing of other actin-associated proteins, we show that this phenotype is not due to altered actin dynamics. Consistent with a role in tip growth, we show that a functional, full-length fusion of monomeric enhanced green fluorescent protein (mEGFP) to myosin XI accumulates at a subcortical, apical region of actively growing protonemal cells.
DWA1 and DWA2, Two Arabidopsis DWD Protein Components of CUL4-Based E3 Ligases, Act Together as Negative Regulators in ABA Signal Transduction
Authors: Lee Jae-Hoon , Yoon Hye-Jin , Terzaghi William , Martinez Cristina , Dai Mingqiu , Li Jigang , Byun Myung-Ok , Deng Xing Wang 
Published: June 2010

Abstract
To elucidate potential roles of CUL4-DDB1-DWD (for Cullin 4-Damaged DNA Binding1-DDB1 binding WD40) E3 ligases in abscisic acid (ABA) signaling, we examined ABA sensitivities of T-DNA mutants of a number of Arabidopsis thaliana DWD genes, which encode substrate receptors for CUL4 E3 ligases. Mutants in two DWD genes, DWA1 and DWA2 (DWD hypersensitive to ABA1 and 2), had ABA-hypersensitive phenotypes. Both proteins interacted with DDB1 in yeast two-hybrid assays and associated with DDB1 and CUL4 in vivo, implying they could form CUL4-based complexes. Several ABA-responsive genes were hyperinduced in both mutants, and the ABA-responsive transcription factors ABA INSENSITIVE 5 (ABI5) and MYC2 accumulated to high levels in the mutants after ABA treatment. Moreover, ABI5 interacted with DWA1 and DWA2 in vivo. Cell-free degradation assays showed ABI5 was degraded more slowly in dwa1 and dwa2 than in wild-type cell extracts. Therefore, DWA1 and/or DWA2 may be the substrate receptors for a CUL4 E3 ligase that targets ABI5 for degradation. Our data indicate that DWA1 and DWA2 can directly interact with each other, and their double mutants exhibited enhanced ABA and NaCl hypersensitivities, implying they can act together. This report thus describes a previously unknown heterodimeric cooperation between two independent substrate receptors for CUL4-based E3 ligases.
Phospholipase A2 Is Required for PIN-FORMED Protein Trafficking to the Plasma Membrane in theArabidopsisRoot
Authors: Lee Ok Ran , Kim Soo Jin , Kim Hae Jin , Hong Jeum Kyu , Ryu Stephen Beungtae , Lee Sang Ho , Ganguly Anindya , Cho Hyung-Taeg 
Published: June 2010

AbstractPhospholipase A2 (PLA2), which hydrolyzes a fatty acyl chain of membrane phospholipids, has been implicated in several biological processes in plants. However, its role in intracellular trafficking in plants has yet to be studied. Here, using pharmacological and genetic approaches, the root hair bioassay system, and PIN-FORMED (PIN) auxin efflux transporters as molecular markers, we demonstrate that plant PLA2s are required for PIN protein trafficking to the plasma membrane (PM) in the Arabidopsis thaliana root. PLA2α, a PLA2 isoform, colocalized with the Golgi marker. Impairments of PLA2 function by PLA2α mutation, PLA2-RNA interference (RNAi), or PLA2 inhibitor treatments significantly disrupted the PM localization of PINs, causing internal PIN compartments to form. Conversely, supplementation with lysophosphatidylethanolamine (the PLA2 hydrolytic product) restored the PM localization of PINs in the pla2α mutant and the ONO-RS-082–treated seedling. Suppression of PLA2 activity by the inhibitor promoted accumulation of trans-Golgi network vesicles. Root hair–specific PIN overexpression (PINox) lines grew very short root hairs, most likely due to reduced auxin levels in root hair cells, but PLA2 inhibitor treatments, PLA2α mutation, or PLA2-RNAi restored the root hair growth of PINox lines by disrupting the PM localization of PINs, thus reducing auxin efflux. These results suggest that PLA2, likely acting in Golgi-related compartments, modulates the trafficking of PIN proteins.