bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of pulmonary embolism using dual-energy computed tomography and correlation with cardiovascular measurements: a preliminary study
Authors: Zhang Long Jiang , Yang Gui Fen , Zhao Yan E. , Zhou Chang Sheng , Lu Guang Ming 
Published: August 2009

Background: Detection of a suspected pulmonary embolism (PE) has been the focus of considerable research over the past few decades. Recently developed dual-source computed tomography (DSCT) scanners with dual-energy mode have been used to detect PE, but the studies on this topic are few. Purpose: To assess the clinical value of dual-source, dual-energy CT (DECT) for the diagnosis of suspected PE and to correlate with cardiovascular measurements. Material and Methods: 31 patients with suspected PE underwent contrast-enhanced DSCT scanning with dual-energy mode. Dedicated software for lung perfusion blood volume (PBV) was used in postprocessing. The numbers and locations of PE in PBV images and CT pulmonary angiography (CTPA) were recorded. Sensitivity and specificity were measured, comparing to CTPA as a standard of reference. The relationship between range of iodine mapping abnormality in PBV images and cardiovascular measurements was analyzed. Results: 33 DECT scans were performed in 31 patients. Seventeen patients had PE, while 14 patients had negative results. Filling defects were detected in pulmonary arteries in 44 pulmonary lobar and 99 segmental arteries. Compared to CTPA as a standard of reference, sensitivity and specificity of PBV images were 93.8% and 93.3% on a per-patient basis, 93.2% and 94.7% on a per-lobe basis, and 76.1% and 97.6% on a per-segment basis, respectively. Spearman correlation test showed good positive correlation between the right ventricle (RV)/left ventricle (LV) diameter ratio and pulmonary lobes with emboli for PBV images ( R=0.663; P=0.004). Conclusion: DECT can provide morphological and functional information of the whole lung in a single contrast-enhanced acquisition; the perfusion defects visualized in PBV images appear to have a positive relationship with the patients’ right heart dysfunction.
Temporal variability in southern North Sea epifauna communities after the cold winter of 1995/1996
Authors: Neumann Hermann , Reiss Henning , Rakers Sebastian , Ehrich Siegfried , Kröncke Ingrid 
Published: August 2009

Abstract
Neumann, H., Reiss, H., Rakers, S., Ehrich, S., and Kröncke, I. 2009. Temporal variability in southern North Sea epifauna communities after the cold winter of 1995/1996. – ICES Journal of Marine Science, 66: 2233–2243. Epifauna communities in the southeastern North Sea were studied from 1998 to 2008 to evaluate the effect of hydroclimatic change in community structure. The spatial analysis revealed four communities along the West and North Frisian coasts, on the Oyster Ground, and on the Dogger Bank. The variability between communities was caused mainly by differing abundance of widespread species such as Asterias rubens, probably reflecting differences in environmental conditions, e.g. temperature variation and food supply. Community structure varied between 1998–2000 and 2003–2008 at the shallow West and North Frisian coasts. The hypothesis is that epibenthic communities in these areas were severely affected by the cold winter of 1995/1996, resulting in the outbreak of the opportunistic brittlestar Ophiura albida and followed by characteristic post-disturbance succession stages from 1998 to 2000. The period between 2003 and 2008 was characterized by a continuous decrease in O. albida and by an increase in other species and diversity in the coastal areas. In contrast, secondary production increased in all four areas after 2003, probably because of an increase in sea surface temperature (SST) and in the length of the warming season. We conclude that the cold winter affected epifauna mainly in shallow areas and that the increasing SST influenced the epifauna in the entire southeastern North Sea mainly through an increased food supply.
Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice
Authors: Andrés Fernando , Galbraith David W. , Talón Manuel , Domingo Concha 
Published: August 2009

Abstract
A great number of plants synchronize flowering with day length. In rice (Oryza sativa), photoperiod is the primary environmental cue that triggers flowering. Here, we show that the s73 mutant, identified in a γ-irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the PHOTOPERIOD SENSITIVITY5 (SE5) gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants show a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of the floral integrator Heading date3a (Hd3a). Early heading date1 (Ehd1), an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds indicated that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering by affecting both Hd1 and Ehd1 flowering pathways.
Plant-Derived Sucrose Is a Key Element in the Symbiotic Association between Trichoderma virens and Maize Plants
Authors: Vargas Walter A. , Mandawe John C. , Kenerley Charles M. 
Published: August 2009

Abstract
Fungal species belonging to the genus Trichoderma colonize the rhizosphere of many plants, resulting in beneficial effects such as increased resistance to pathogens and greater yield and productivity. However, the molecular mechanisms that govern the recognition and association between Trichoderma and their hosts are still largely unknown. In this report, we demonstrate that plant-derived sucrose (Suc) is an important resource provided to Trichoderma cells and is also associated with the control of root colonization. We describe the identification and characterization of an intracellular invertase from Trichoderma virens (TvInv) important for the mechanisms that control the symbiotic association and fungal growth in the presence of Suc. Gene expression studies revealed that the hydrolysis of plant-derived Suc in T. virens is necessary for the up-regulation of Sm1, the Trichoderma-secreted elicitor that systemically activates the defense mechanisms in leaves. We determined that as a result of colonization of maize (Zea mays) roots by T. virens, photosynthetic rate increases in leaves and the functional expression of tvinv is crucial for such effect. In agreement, the steady-state levels of mRNA for Rubisco small subunit and the oxygen-evolving enhancer 3-1 were increased in leaves of plants colonized by wild-type T. virens. We conclude that during the symbiosis, the sucrolytic activity in the fungal cells affects the sink activity of roots, directing carbon partitioning toward roots and increasing the rate of photosynthesis in leaves. A discussion of the role of Suc in controlling the fungal proliferation on roots and its pivotal role in the coordination of plant-microbe associations is provided.
Quantitative Proteomics of Seed Filling in Castor: Comparison with Soybean and Rapeseed Reveals Differences between Photosynthetic and Nonphotosynthetic Seed Metabolism
Authors: Houston Norma L. , Hajduch Martin , Thelen Jay J. 
Published: August 2009

Abstract
Seed maturation or seed filling is a phase of development that plays a major role in the storage reserve composition of a seed. In many plant seeds photosynthesis plays a major role in this process, although oilseeds, such as castor (Ricinus communis), are capable of accumulating oil without the benefit of photophosphorylation to augment energy demands. To characterize seed filling in castor, a systematic quantitative proteomics study was performed. Two-dimensional gel electrophoresis was used to resolve and quantify Cy-dye-labeled proteins expressed at 2, 3, 4, 5, and 6 weeks after flowering in biological triplicate. Expression profiles for 660 protein spot groups were established, and of these, 522 proteins were confidently identified by liquid chromatography-tandem mass spectrometry by mining against the castor genome. Identified proteins were classified according to function, and the most abundant groups of proteins were involved in protein destination and storage (34%), energy (19%), and metabolism (15%). Carbon assimilatory pathways in castor were compared with previous studies of photosynthetic oilseeds, soybean (Glycine max) and rapeseed (Brassica napus). These comparisons revealed differences in abundance and number of protein isoforms at numerous steps in glycolysis. One such difference was the number of enolase isoforms and their sum abundance; castor had approximately six times as many isoforms as soy and rapeseed. Furthermore, Rubisco was 11-fold less prominent in castor compared to rapeseed. These and other differences suggest some aspects of carbon flow, carbon recapture, as well as ATP and NADPH production in castor differs from photosynthetic oilseeds.
Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night
Authors: Meyer Etienne H. , Tomaz Tiago , Carroll Adam J. , Estavillo Gonzalo , Delannoy Etienne , Tanz Sandra K. , Small Ian D. , Pogson Barry J. , Millar A. Harvey 
Published: August 2009

Abstract
Respiratory oxidative phosphorylation is a cornerstone of cellular metabolism in aerobic multicellular organisms. The efficiency of this process is generally assumed to be maximized, but the presence of dynamically regulated nonphosphorylating bypasses implies that plants can alter phosphorylation efficiency and can benefit from lowered energy generation during respiration under certain conditions. We characterized an Arabidopsis (Arabidopsis thaliana) mutant, ndufs4 (for NADH dehydrogenase [ubiquinone] fragment S subunit 4), lacking complex I of the respiratory chain, which has constitutively lowered phosphorylation efficiency. Through analysis of the changes to mitochondrial function as well as whole cell transcripts and metabolites, we provide insights into how cellular metabolism flexibly adapts to reduced phosphorylation efficiency and why this state may benefit the plant by providing moderate stress tolerance. We show that removal of the single protein subunit NDUFS4 prevents assembly of complex I and removes its function from mitochondria without pleiotropic effects on other respiratory components. However, the lack of complex I promotes broad changes in the nuclear transcriptome governing growth and photosynthetic function. We observed increases in organic acid and amino acid pools in the mutant, especially at night, concomitant with alteration of the adenylate content. While germination is delayed, this can be rescued by application of gibberellic acid, and root growth assays of seedlings show enhanced tolerance to cold, mild salt, and osmotic stress. We discuss these observations in the light of recent data on the knockout of nonphosphorylating respiratory bypass enzymes that show opposite changes in metabolites and stress sensitivity. Our data suggest that the absence of complex I alters the adenylate control of cellular metabolism.
Protective effects of affinity‐purified antibody and truncated vaccines against Pseudomonas aeruginosa V‐antigen in neutropenic mice
Authors: Moriyama Kiyoshi , Wiener‐Kronish Jeanine P. , Sawa Teiji 
Published: August 2009

ABSTRACTVirulent P. aeruginosa strains express PcrV, one of the translocational components of the type III secretion system. PcrV has been reported to be a protective antigen against lethal P. aeruginosa infection. The PcrV region, which contributes to protective immunity against P. aeruginosa infection, was investigated by using genetically engineered, truncated PcrV proteins and affinity‐purified anti‐PcrV antibodies against the truncated PcrV proteins. The efficacy of active and passive immunization against PcrV was tested in mice with cyclophosphamide‐induced immunosuppression by intraabdominal challenge of P. aeruginosa. Active immunization with either full‐length PcrV1‐294 or PcrV139‐294 significantly improved the survival of mice infected with P. aeruginosa, while PcrV139‐258, PcrV139‐234, PcrV197‐294, and PcrV261‐294 were not protective. These results suggest that an effective PcrV vaccine needs to contain not only the Mab166 epitope (PcrV144‐257) but also the carboxyl terminal tail of PcrV. In the case of passive immunization, administration of affinity‐purified anti‐PcrV IgG against either PcrV1‐294 or PcrV139‐258 showed significantly higher efficacy against lethal P. aeruginosa infection than did original anti‐PcrV IgG and Mab166. The increased efficacy of affinity‐purified anti‐PcrV IgG implies that more potent anti‐PcrV strategies are possible. The results of this study are crucial to the development of an effective PcrV vaccine for active immunization and to an appropriate blocking anti‐PcrV antibody against P. aeruginosa infection in humans.
Anti‐myeloma activity of the novel 2‐aminothienopyrimidine Hsp90 inhibitor NVP‐BEP800
Authors: Stühmer Thorsten , Chatterjee Manik , Grella Evelyn , Seggewiss Ruth , Langer Christian , Müller Sabine , Schoepfer Joseph , Garcia‐Echeverria Carlos , Quadt Cornelia , Jensen Michael R. , Einsele Hermann , Bargou Ralf C. 
Published: August 2009

SummaryThe 90 kD heat shock protein (Hsp90) molecular chaperone sustains multiple components of oncogenic pathways and has recently emerged as a therapeutic target that is now being clinically tested in a number of malignancies. In order to address formulation issues and to deal with possible resistance mechanisms against small molecule Hsp90 inhibitors, a range of compounds based on different molecular scaffolds are now being developed. The present study preclinically tested the effects of the novel 2‐aminothienopyrimidine class Hsp90 inhibitor NVP‐BEP800, which is suitable for oral formulations, on multiple myeloma cells from established cell lines and on a larger cohort (n = 40) of primary myeloma samples. The drug effectively and specifically killed the majority of primary myeloma cells in coculture with bone marrow stromal cells and reliably entailed molecular consequences of Hsp90 blockade – such as survival pathway breakdown and client protein depletion – in multiple myeloma cells from cell lines as well as from patients. Collectively, the properties of this novel drug support clinical testing in multiple myeloma.
A morphological classification capturing functional variation in phytoplankton
Authors: KRUK CARLA , HUSZAR VERA L. M. , PEETERS EDWIN T. H. M. , BONILLA SYLVIA , COSTA LUCIANA , LÜRLING MIQUEL , REYNOLDS COLIN S. , SCHEFFER MARTEN 
Published: August 2009

Summary1. A logical way of distinguishing functional groups of phytoplankton is to cluster species according to their functional traits, such as growth rate and nutrient assimilation constants. However, data for such an approach are lacking for the vast majority of the species.2. In this study, we show that a classification based on simple morphological traits may capture much of the variability in functional properties among the phytoplankton. We used information on more than 700 freshwater species, from more than 200 lakes situated in climate zones ranging from subpolar to tropical.3. Morphological characteristics correlated well with functional properties, such as growth rate and sinking rate, and also with the population size and biomass attained in the field. This suggests that morphology is a good predictor of the functional characteristics of species.4. Cluster analysis was used to define seven species groups based on morphology. Although some of the clusters are taxonomically homogeneous, others include species of several separate divisions. Functional traits (not used for the classification) differed significantly among the clusters, suggesting that the clusters may indeed represent meaningful functional groups.5. Advantages of our morphological approach to classification include its objectivity, its independence from taxonomic affiliations, and the relative ease of its application to the majority of species for which physiological traits are unknown and are not readily determined.
The role of electronic pocket dictionaries as an English learning tool among Chinese students
Authors: Jian Hua‐Li , Sandnes Frode Eika , Law Kris M. Y. , Huang Yo‐Ping , Huang Yueh‐Min 
Published: August 2009

AbstractThis study addressed the role of electronic pocket dictionaries as a language learning tool among university students in Hong Kong and Taiwan. The target groups included engineering and humanities students at both undergraduate and graduate level. Speed of reference was found to be the main motivator for using an electronic pocket dictionary. Next, the functionality used was found to be connected to the language proficiency of the learner. Finally, multimedia content was ranked least important. The results of this study have implications for the design of electronic dictionaries and for the teaching of second languages with electronic dictionaries. In particular, device developers should focus on improving the accessing speed and pay less attention to multimedia functionality. Educators should ensure that the device functionality matches the language proficiency level of the students.
Factor structure of the Athens Insomnia Scale and its associations with demographic characteristics and depression in adolescents
Authors: YEN CHENG‐FANG , KING BRYAN H. , CHANG YU‐PING 
Published: August 2009

SummaryThe eight‐item Athens Insomnia Scale (AIS‐8) is an instrument that has been used frequently to assess insomnia problems. Previous research on adults has found that the AIS‐8 functioned as a sole component. This study aimed to examine the prevalence rates of insomnia problems on the AIS‐8, the factor structure of the AIS‐8 in adolescents and its associations with demographic characteristics and depression in adolescents. A total of 8319 adolescent students (4334 girls and 3985 boys, mean age = 14.7 years, standard deviation = 1.7 years) in southern Taiwan were recruited into this study and completed the AIS‐8. We performed an exploratory factor analysis to examine the factor structure of the AIS‐8, and used the parallel analysis for making decisions regarding factor retention. We also used multiple regression analysis models to determine the associations between insomnia and demographic characteristics and depression. The results found that a high proportion of adolescents had insomnia problems as measured by the AIS‐8. The AIS‐8 was composed of two different factors when used among a large adolescent population, including insomnia symptoms (factor 1) and subjective sleep and daytime distress (factor 2). While being male, being younger, and having depression were associated positively with the severity of insomnia symptoms (factor 1), being older, living in urban areas, and having depression were associated positively with the severity of subjective sleep and daytime distress (factor 2). Clinicians and researchers should consider the different meanings of the two factors of the AIS‐8 when using this tool to assess insomnia problems in adolescents.
Sleep state distribution of obstructive events in children: is obstructive sleep apnoea really a rapid eye movement sleep‐related condition?
Authors: VERGINIS NICOLE , JOLLEY DAMIEN , HORNE ROSEMARY S. C. , DAVEY MARGOT J. , NIXON GILLIAN M. 
Published: August 2009

SummaryObstructive sleep apnoea (OSA) in children is commonly considered to occur predominantly in rapid eye movement (REM) sleep, but clinical experience suggests that this is not universally the case. We hypothesized that there would be a subgroup of children with OSA who have non‐REM (NREM) predominance of obstructive events and that these children share certain clinical characteristics. Thus, we aimed to compare the obstructive apnoea–hypopnoea index (OAHI) in REM versus NREM sleep and to assess factors influencing the distribution of events by sleep state. Polysomnography (PSG) recordings of 102 children aged 0–18 years with moderate to severe OSA (OAHI ≥5 h−1) were reviewed. OAHI was calculated separately for REM and NREM sleep. A REM predominance index (RPI) was determined using log transformation [RPI = log (REM OAHI + 0.5) − log (NREM OAHI + 0.5)] and compared with possible influencing factors using multiple linear regression. Analysis showed that obstructive events were more common in REM sleep (median REM OAHI 21.4 h−1, median NREM OAHI 8.3 h−1, P < 0.001). Mean RPI was significantly greater than zero (P = 0.003). However, a substantial minority of children (30.4%) had a higher NREM than REM OAHI. The factors that were related significantly to NREM predominance were older age (P = 0.02), higher arousal index (P < 0.001) and higher SpO2 nadir (P < 0.001). Our findings demonstrate that while OSA is a REM sleep‐related problem in the majority of children, there is a significant subset of children with NREM predominance of obstructive events. This finding highlights the importance of considering sleep state distribution of events in studies of the pathophysiology and outcomes of OSA in childhood.
Switching off small RNA regulation with trap‐mRNA
Authors: Overgaard Martin , Johansen Jesper , Møller‐Jensen Jakob , Valentin‐Hansen Poul 
Published: August 2009

SummarySmall non‐coding regulatory RNAs in bacteria have been shown predominantly to be tightly regulated at the level of transcription initiation, and sRNAs that function by an antisense mechanism on trans‐encoded target mRNAs have been shown or predicted to act stoichiometrically. Here we show that MicM, which silences the expression of an outer membrane protein, YbfM under most growth conditions, does not become destabilized by target mRNA overexpression, indicating that the small RNA regulator acts catalytically. Furthermore, our regulatory studies suggested that control of micM expression is unlikely to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA‐based regulatory principle in which induction of a trap‐mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA‐based silencing of its cognate target mRNA. In the present case, antisense regulation by chb mRNA of the antisense regulator MicM by an extended complementary sequence element, results in induction of ybfM mRNA translation. This type of regulation is reminiscent of the regulation of microRNA activity through target mimicry that occurs in plants.
Targeted σ factor turnover inserts negative control into a positive feedback loop
Authors: Donohue Timothy J. 
Published: August 2009

SummarySince their classification as members of the σ70 superfamily, Group IV alternative σ factors have been found to control gene expression in response to diverse environmental or stress signals. Activity of the Streptomyces coelicolor Group IV family member, σR (SigR), is increased by changes in the oxidation‐reduction state of cytoplasmic disulphide bonds. Once released by its cognate anti‐σ factor RsrA, σR activates expression of gene products that help cells reduce cytoplasmic disulphide bonds. In this issue of Molecular Microbiology, Kim and co‐workers provide new insights into positive and negative control of σR activity. The authors show that a transcript derived from the inducible σR‐dependent sigRrsrA p2 promoter operon encodes a σR protein of a higher molecular weight (termed σR′) than is found in uninduced cells. One major difference between σR′ and the smaller σR protein found in uninduced cells is the rapid proteolysis of σR′ by the ClpP1/P2 protease system. The genes for the ClpP1/ClpP2 protease subunits are themselves members of the σR regulon. The newly identified positive (σR′ synthesis) and negative control (selective σR′ turnover) aspects of this circuit are either found or predicted to exist in other related Group IV σ factor family members.