bluuebunny/crossref_metadata_2025_split huggingface dataset:
SplamiR—prediction of spliced miRNAs in plants
Authors: Thieme Christoph J. , Gramzow Lydia , Lobbes Dajana , Theißen Günter 
Published: March 2011

Abstract
Motivation: MicroRNAs (miRNAs) are important regulators of biological processes in plants and animals. Recently, miRNA genes have been discovered, whose primary transcripts are spliced and which cannot be predicted directly from genomic sequence. Hence, more sophisticated programs for the detection of spliced miRNAs are required.
Results: Here, we present the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem–loop structures. Next, in silico splice variants of database sequences with complementarity to an mRNA of interest are classified as to whether they could represent miRNAs targeting this mRNA. Our method identifies all known cases of spliced miRNAs in rice, and a previously undiscovered miRNA in maize which is supported by an expressed sequence tag (EST). SplamiR permits identification of spliced miRNAs for a given target mRNA in many plant genomes.
Availability: The program is freely available at http://www.uni-jena.de/SplamiR.html.
Contact: guenter.theissen@uni-jena.de
Supplementary information: Supplementary data are available at Bioinformatics online.
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns
Authors: Yang Xinan , Li Jianrong , Lee Younghee , Lussier Yves A. 
Published: March 2011

Abstract
Summary: GO-Module is a web-accessible synthesis and visualization tool developed for end-user biologists to greatly simplify the interpretation of prioritized Gene Ontology (GO) terms. GO-Module radically reduces the complexity of raw GO results into compact biomodules in two distinct ways, by (i) constructing biomodules from significant GO terms based on hierarchical knowledge, and (ii) refining the GO terms in each biomodule to contain only true positive results. Altogether, the features (biomodules) of GO-Module outputs are better organized and on average four times smaller than the input GO terms list (P = 0.0005, n = 16).
Availability: http://lussierlab.org/GO-Module
Contact: ylussier@bsd.uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition
Authors: Bécavin Christophe , Tchitchek Nicolas , Mintsa-Eya Colette , Lesne Annick , Benecke Arndt 
Published: March 2011

Abstract
Motivation: Multidimensional scaling (MDS) is a well-known multivariate statistical analysis method used for dimensionality reduction and visualization of similarities and dissimilarities in multidimensional data. The advantage of MDS with respect to singular value decomposition (SVD) based methods such as principal component analysis is its superior fidelity in representing the distance between different instances specially for high-dimensional geometric objects. Here, we investigate the importance of the choice of initial conditions for MDS, and show that SVD is the best choice to initiate MDS. Furthermore, we demonstrate that the use of the first principal components of SVD to initiate the MDS algorithm is more efficient than an iteration through all the principal components. Adding stochasticity to the molecular dynamics simulations typically used for MDS of large datasets, contrary to previous suggestions, likewise does not increase accuracy. Finally, we introduce a k nearest neighbor method to analyze the local structure of the geometric objects and use it to control the quality of the dimensionality reduction.
Results: We demonstrate here the, to our knowledge, most efficient and accurate initialization strategy for MDS algorithms, reducing considerably computational load. SVD-based initialization renders MDS methodology much more useful in the analysis of high-dimensional data such as functional genomics datasets.
Contact: arndt@ihes.fr
Development and evaluation of a cpue-based harvest control rule for the southern and eastern scalefish and shark fishery of Australia
Authors: Little L. Richard , Wayte Sally E. , Tuck Geoffrey N. , Smith Anthony D. M. , Klaer Neil , Haddon Malcolm , Punt André E. , Thomson Robin , Day Jemery , Fuller Mike 
Published: March 2011

Abstract
Little, L. R., Wayte, S. E., Tuck, G. N., Smith, A. D. M., Klaer, N., Haddon, M., Punt, A. E., Thomson, R., Day, J., and Fuller, M. 2011. Development and evaluation of a cpue-based harvest control rule for the southern and eastern scalefish and shark fishery of Australia. – ICES Journal of Marine Science, 68: 1699–1705. Many fishery management agencies are adopting harvest control rules (HCRs) to achieve harvest policies and management objectives. HCRs, however, often require data-intensive stock assessments to facilitate the harvest prescription. An HCR based on catch and catch per unit effort (cpue) was developed for the southern and eastern scalefish and shark fishery of Australia, for stocks that lack the data needed to conduct a full statistical catch-at-age assessment. The HCR produces a recommended biological catch and is characterized by two parameters, target cpue and target catch, both derived from historical data. Simulation tests showed that the HCR could guide the stock to the desired state from different initial levels of depletion. However, the selection of parameter values for the HCR was critical. Achieving fishery objectives was difficult when the target catch was a function of recent catch, rather than data from a predefined historical reference period. Problems may also arise when specifying the reference period on which the HCR parameters are determined. The cpue-based HCR is a valuable tool for managing fisheries where monitoring and assessment activities are relatively expensive, or in general, where data are scarce.
Myocardial Blood Flow during General Anesthesia with Xenon in Humans
Authors: Schaefer Wolfgang , Meyer Philipp T. , Rossaint Rolf , Baumert Jan H. , Coburn Mark , Fries Michael , Rex Steffen 
Published: March 2011

Background
Xenon has only minimal hemodynamic side effects and induces pharmacologic preconditioning. Thus, the use of xenon could be an interesting option in patients at risk for perioperative myocardial ischemia. However, little is known about the effects of xenon anesthesia on myocardial blood flow (MBF) and coronary vascular resistance in humans.

Methods
Myocardial blood flow was noninvasively quantified by H₂¹⁵O positron emission tomography in six healthy volunteers (age: 38 ± 8 yr). MBF was measured at baseline and during general anesthesia induced with propofol and maintained with xenon, 59 ± 0%. Absolute quantification of MBF was started after the calculated plasma concentration of propofol had decreased to less than 1.5 μg · ml⁻¹.

Results
Compared with baseline (MBFbaseline, 1.03 ± 0.09 ml · min⁻¹ · g⁻¹; mean ± SD), MBF was decreased insignificantly by xenon (MBFxenon, 0.80 ± 0.22 ml · min⁻¹ · g⁻¹; -21%, P = 0.11). Xenon decreased the rate-pressure product (RPP; heart rate × systolic arterial pressure), an indicator of cardiac work and myocardial oxygen consumption (-15%, P < 0.04). When correcting for the RPP, the decrease in MBF observed during xenon anesthesia was reduced to -9% (MBFcorr-xenon, 1.42 ± 0.28 ml · g⁻¹ · mmHg⁻¹ vs. MBFcorr-baseline, 1.60 ± 0.28 ml · g⁻¹ · mmHg⁻¹, P = 0.32). Xenon did not affect the dependency of MBF on the RPP. Coronary vascular resistance did not significantly change (+15 ± 23%, P = 0.18) during xenon anesthesia.

Conclusions
In healthy subjects, xenon has only minimal effects on coronary flow dynamics. These effects are probably of indirect nature, reflecting the decrease in myocardial oxygen consumption induced by the effects of xenon anesthesia on cardiac work.
Effects of Volatile and Intravenous Anesthesia on the Alveolar and Systemic Inflammatory Response in Thoracic Surgical Patients
Authors: Schilling Thomas , Kozian Alf , Senturk Mert , Huth Christof , Reinhold Annegret , Hedenstierna Göran , Hachenberg Thomas 
Published: March 2011

Background
One-lung ventilation (OLV) results in alveolar proinflammatory effects, whereas their extent may depend on administration of anesthetic drugs. The current study evaluates the effects of different volatile anesthetics compared with an intravenous anesthetic and the relationship between pulmonary and systemic inflammation in patients undergoing open thoracic surgery.

Methods
Sixty-three patients scheduled for elective open thoracic surgery were randomized to receive anesthesia with 4 mg · kg⁻¹ · h⁻¹ propofol (n = 21), 1 minimum alveolar concentration desflurane (n = 21), or 1 minimum alveolar concentration sevoflurane (n = 21). Analgesia was provided by remifentanil (0.25 μg · kg⁻¹ · min⁻¹). After intubation, all patients received pressure-controlled mechanical ventilation with a tidal volume of approximately 7 ml · kg ideal body weight, a peak airway pressure lower than 30 cm H₂O, a respiratory rate adjusted to a Paco2 of 40 mmHg, and a fraction of inspired oxygen lower than 0.8 during OLV. Fiberoptic bronchoalveolar lavage of the ventilated lung was performed immediately after intubation and after surgery. The expression of inflammatory cytokines was determined in the lavage fluids and serum samples by multiplexed bead-based immunoassays.

Results
Proinflammatory cytokines increased in the ventilated lung after OLV. Mediator release was more enhanced during propofol anesthesia compared with desflurane or sevoflurane administration. For tumor necrosis factor-α, the values were as follows: propofol, 5.7 (8.6); desflurane, 1.6 (0.6); and sevoflurane, 1.6 (0.7). For interleukin-8, the values were as follows: propofol, 924 (1680); desflurane, 390 (813); and sevoflurane, 412 (410). (Values are given as median [interquartile range] pg · ml⁻¹). Interleukin-1β was similarly reduced during volatile anesthesia. The postoperative serum interleukin-6 concentration was increased in all patients, whereas the systemic proinflammatory response was negligible.

Conclusions
OLV increases the alveolar concentrations of proinflammatory mediators in the ventilated lung. Both desflurane and sevoflurane suppress the local alveolar, but not the systemic, inflammatory responses to OLV and thoracic surgery.
Sphingolipids in the Root Play an Important Role in Regulating the Leaf Ionome inArabidopsis thaliana
Authors: Chao Dai-Yin , Gable Kenneth , Chen Ming , Baxter Ivan , Dietrich Charles R. , Cahoon Edgar B. , Guerinot Mary Lou , Lahner Brett , Lü Shiyou , Markham Jennifer E. , Morrissey Joe , Han Gongshe , Gupta Sita D. , Harmon Jeffrey M. , Jaworski Jan G. , Dunn Teresa M. , Salt David E. 
Published: March 2011

AbstractSphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10Δ mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B mutants. Although the 3-KDS reductase genes are functionally redundant and ubiquitously expressed in Arabidopsis, 3-KDS reductase activity was reduced to 10% of wild-type levels in the loss-of-function tsc10a mutant, leading to an altered sphingolipid profile. This perturbation of sphingolipid biosynthesis in the Arabidopsis tsc10a mutant leads an altered leaf ionome, including increases in Na, K, and Rb and decreases in Mg, Ca, Fe, and Mo. Reciprocal grafting revealed that these changes in the leaf ionome are driven by the root and are associated with increases in root suberin and alterations in Fe homeostasis.
AUXIN RESPONSE FACTOR8 RegulatesArabidopsisPetal Growth by Interacting with the bHLH Transcription Factor BIGPETALp
Authors: Varaud Emilie , Brioudes Florian , Szécsi Judit , Leroux Julie , Brown Spencer , Perrot-Rechenmann Catherine , Bendahmane Mohammed 
Published: March 2011

AbstractPlant organ growth and final size are determined by coordinated cell proliferation and expansion. The BIGPETALp (BPEp) basic helix-loop-helix (bHLH) transcription factor was shown to limit Arabidopsis thaliana petal growth by influencing cell expansion. We demonstrate here that BPEp interacts with AUXIN RESPONSE FACTOR8 (ARF8) to affect petal growth. This interaction is mediated through the BPEp C-terminal domain (SDBPEp) and the C-terminal domain of ARF8. Site-directed mutagenesis identified an amino acid consensus motif in SDBPEp that is critical for mediating BPEp-ARF8 interaction. This motif shares sequence similarity with motif III of ARF and AUXIN/INDOLE-3-ACETIC ACID proteins. Petals of arf8 mutants are significantly larger than those of the wild type due to increased cell number and increased cell expansion. bpe arf8 double mutant analyses show that during early petal development stages, ARF8 and BPEp work synergistically to limit mitotic growth. During late stages, ARF8 and BPEp interact to limit cell expansion. The alterations in cell division and cell expansion observed in arf8 and/or bpe mutants are associated with a change in expression of early auxin-responsive genes. The data provide evidence of an interaction between an ARF and a bHLH transcription factor and of its biological significance in regulating petal growth, with local auxin levels likely influencing such a biological function.
APO1 Promotes the Splicing of Chloroplast Group II Introns and Harbors a Plant-Specific Zinc-Dependent RNA Binding Domain
Authors: Watkins Kenneth P. , Rojas Margarita , Friso Giulia , van Wijk Klaas J. , Meurer Jörg , Barkan Alice 
Published: March 2011

Abstract
Arabidopsis thaliana APO1 is required for the accumulation of the chloroplast photosystem I and NADH dehydrogenase complexes and had been proposed to facilitate the incorporation of [4Fe-4S] clusters into these complexes. The identification of maize (Zea mays) APO1 in coimmunoprecipitates with a protein involved in chloroplast RNA splicing prompted us to investigate a role for APO1 in splicing. We show here that APO1 promotes the splicing of several chloroplast group II introns: in Arabidopsis apo1 mutants, ycf3-intron 2 remains completely unspliced, petD intron splicing is strongly reduced, and the splicing of several other introns is compromised. These splicing defects can account for the loss of photosynthetic complexes in apo1 mutants. Recombinant APO1 from both maize and Arabidopsis binds RNA with high affinity in vitro, demonstrating that DUF794, the domain of unknown function that makes up almost the entirety of APO1, is an RNA binding domain. We provide evidence that DUF794 harbors two motifs that resemble zinc fingers, that these bind zinc, and that they are essential for APO1 function. DUF794 is found in a plant-specific protein family whose members are all predicted to localize to mitochondria or chloroplasts. Thus, DUF794 adds a new example to the repertoire of plant-specific RNA binding domains that emerged as a product of nuclear-organellar coevolution.
Optimization of geometric parameters of latticed structures using genetic algorithm
Authors: Hashemian Amir H. , Kargarnovin Mohammad H. , Jam Jafar E. 
Published: March 2011

PurposeThe purpose of this paper is to analyze a squared lattice cylindrical shell under compressive axial load and to optimize the geometric parameters to achieve the maximum buckling load. Also a comparison between buckling loads of a squared lattice cylinder and a solid hollow cylinder with equal weight, length and outer diameter is performed to reveal the superior performance of the squared lattice cylindrical shells.Design/methodology/approachA cylindrical lattice shell includes circumferential and longitudinal rods with geometric parameters such as cross‐section areas of the rods, distances and angles between them. In this study, the governing differential equation for buckling load which can be presumed as a criterion for designing lattice structures with a specific weight is derived and is used as an objective function in genetic algorithm (GA) method to calculate the optimum geometric parameters of the shell. The optimum parameters were modelled in finite element method (FEM) in order to verify the buckling loads obtained from GA. In another effort, the FEM was applied to analyze the solid hollow cylinders.FindingsThe results demonstrate relatively close agreement between the buckling loads obtained from GA and FEM for such shells. It was also shown that latticed cylinders have better performance to carry compressive axial loads than the equivalent solid hollow cylinders with equal weights, lengths and outer diameters.Research limitations/implicationsThe studies reported in this paper have been carried out for a single squared lattice shell without using two‐side skins. However, using skins can give better performance in carrying compressive axial loads.Practical implicationsThe results in this paper show that this type of effective, economical lightweight and functional structures could be applied as inter‐stages, inter‐tanks, aircraft fuselage, rocket motor cases, pressure vessels and other elements of civil engineering structures in order to have greater strength and lower weight.Originality/valueSquared lattice cylindrical shell with optimum geometric design could provide the chance for eliminating the stiffeners of shells in aerospace structures in order to decrease the weight and increase the load‐bearing capacity.
Outgassing studies on thermal control coatings for micro‐satellites
Authors: Chandrakant Joshi Sunil 
Published: March 2011

PurposeWith the advent of micro‐satellites technology, passive thermal controls in the form of surface coatings have become important for onboard thermal management. The thermal coatings, however, suffer outgassing and mass loss due to their direct exposure to harsh thermal environment and high vacuum in space. The purpose of this paper is to discuss testing and evaluation on outgassing of AA6061‐T6 specimen surfaces treated with various types of anodized coatings of different thicknesses and the related mass loss before and after thermal exposure.Design/methodology/approachSamples of chromic acid, polytetrafluroethylene polymer, and black‐ and brown‐colour anodized aluminum coupons were subjected to high vacuum (∼1×10−6 mbar), before and after thermal baking at 120°C. Spectrum analysis of the outgassed material to know their quantities and proportion was conducted subsequently using a Quadrupole mass analyzer.FindingsThe surface coatings under study complied with the spacecraft requirements for the mass loss of less than 1 percent of the total mass of the coating material used for that surface. The mass spectrum analysis of the outgassed material indicated that the majority of the coating mass loss was on account of water vapours and organic solvents like ethylene.Practical implicationsThese results provided a good insight into the reliability of the coating materials studied and the bonding between the aluminum substrates and the coatings.Originality/valueThe coatings and the technology needed for their application on aluminum are readily available. The present work on outgassing and mass loss in a simulated space environment will provide useful insight on their usage for micro‐satellites.
Validation of comprehensive dynamics analysis predictions for a rotor in descending flight
Authors: Park Jae S. , Jung Sung N. , You Young H. , Park Soo H. , Yu Yung H. 
Published: March 2011

PurposeThe purpose of this paper is to evaluate the prediction capability of comprehensive structural dynamics (CSD) analysis codes for the higher harmonic control aeroacoustic rotor test (HART) II data.Design/methodology/approachA nonlinear flexible multibody dynamics analysis code DYMORE, as well as the comprehensive analytical model of rotorcraft aerodynamics and dynamics (CAMRAD) II, are used to perform the task. The predicted results on rotating free vibration analysis, airloads, blade elastic motions, and structural moments are correlated with the measured data for the baseline, minimum noise, and minimum vibration cases.FindingsThe DYMORE analysis results with a free wake model show a good performance in capturing blade vortex interaction peaks in the prediction of section normal forces but apparently with a phase shift problem. The high‐frequency behavior in the airloads signal does not affect much on the aeroelastic response and structural moments of the rotor.Originality/valueThe present approach uses two separate CSD codes to systematically validate the HART II data. The accuracy of each code on structural dynamic aspects of HART II rotor is assessed using a consistent set of inputs. The effects of blade tip deflections on the interaction of blades and their trailed vortices leading to a reduced noise emission are also investigated.
Optical flow‐based obstacle avoidance of a fixed‐wing MAV
Authors: Rezaei Mahdi , Saghafi Fariborz 
Published: March 2011

PurposeThe purpose of this paper is to describe optical flow‐based navigation of a very light fixed‐wing aircraft in flight between obstacles.Design/methodology/approachThe optical flow information of two cameras mounted on the aircraft is used to detect the obstacle. It is assumed that the image processing has been completed and the optical flow vectors have been obtained beforehand. The optical flow is used to detect the obstacles and make a rapid turn manoeuvre for the aircraft.FindingsIt is shown that using the optical flow feedback by itself is unable to give a rapid turn to the aircraft and its rate should be employed into the control law. Six degree‐of‐freedom flight simulation showed that the proposed navigation and control strategy give satisfactory results in different flight environments like corridors with parallel and non‐parallel walls and in the L junctions. Simulations also showed that the aircraft flight velocity has little effect on collision avoidance performance.Practical implicationsThis paper provides a theoretical framework to study the different parameters affect the obstacle detection and avoidance of an aircraft.Originality/valueAn analytical equation has been developed to relate the obstacle detection distance to the aircraft manoeuvrability parameters. In addition, an optical flow‐based controller also has been designed to provide rapid turn manoeuvres using the aileron control surface.