bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice
Authors: Robb Sofia M C , Lu Lu , Valencia Elizabeth , Burnette James M , Okumoto Yutaka , Wessler Susan R , Stajich Jason E
Published: April 2013

Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events. It does this by comparing the numbers of RelocaTE aligned reads to reads that map to the same genomic position without the TE. Although RelocaTE and CharacTErizer can be used for any TE, they were developed to analyze the very active mPing element which is undergoing massive amplification in specific strains of Oryza sativa (rice). Three individuals of one of these strains, A123, were resequenced and analyzed for mPing insertion site polymorphisms. The majority of mPing insertions found (~97%) are not present in the reference, and two siblings from a self-crossed of this strain were found to share only ~90% of their insertions. Private insertions are primarily heterozygous but include both homozygous and predicted somatic insertions. The reliability of the predicted genotypes was validated by polymerase chain reaction.
Genetic Polymorphisms in Host Innate Immune Sensor Genes and the Risk of Nasopharyngeal Carcinoma in North Africa
Authors: Moumad Khalid , Lascorz Jesus , Bevier Melanie , Khyatti Meriem , Ennaji Moulay Mustapha , Benider Abdellatif , Huhn Stefanie , Lu Shun , Chouchane Lotfi , Corbex Marilys , Hemminki Kari , Försti Asta
Published: April 2013

Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world. It is an Epstein-Barr virus−associated malignancy with an unusual racial and geographical distribution. The host innate immune sensor genes play an important role in infection recognition and immune response against viruses. Therefore, we examined the association between polymorphisms in genes within a group of pattern recognition receptors (including families of Toll-like receptors, C-type lectin receptors, and retinoic acid−inducible gene I−like receptors) and NPC susceptibility. Twenty-six single-nucleotide polymorphisms (SNPs) in five pattern-recognition genes were genotyped in 492 North African NPC cases and 373 frequency-matched controls. TLR3_rs3775291 was the most significantly associated SNP (odds ratio [OR] 1.49; 95% confidence interval [95% CI] 1.11−2.00; P = 0.008; dominant model). The analysis showed also that CD209_rs7248637 (OR 0.69; 95% CI 0.52−0.93; P = 0.02; dominant model) and DDX58_rs56309110 (OR 0.70; 95% CI 0.51−0.98; P = 0.04) were associated with the risk of NPC. An 18% increased risk per allele was observed for the five most significantly associated SNPs, TLR3_rs3775291, CD209_rs7248637, DDX58_rs56309110, CD209_rs4804800, and MBL2_rs10824792, (ptrend = 8.2 × 10−4). Our results suggest that genetic variation in pattern-recognition genes is associated with the risk of NPC. These preliminary findings require replication in larger studies.
A Nucleosomal Region Important for Ensuring Proper Interactions Between the Transcription Elongation Factor Spt16 and Transcribed Genes inSaccharomyces cerevisiae
Authors: Nguyen Hoai-Trang T , Wharton William , Harper Jennifer A , Dornhoffer James R , Duina Andrea A
Published: April 2013

The highly conserved FACT (FAcilitates Chromatin Transactions) histone chaperone assists in the transcription elongation process first by facilitating the removal of histones in front of transcribing RNA polymerase II (Pol II) and then by contributing to nucleosome reassembly in the wake of Pol II passage. Whereas it is well established that FACT localizes across actively transcribed genes, the mechanisms that regulate FACT recruitment to and disengagement from chromatin during transcription still remain to be elucidated. Using the Saccharomyces cerevisiae model system, we previously showed that a histone H3 mutant—H3-L61W—greatly perturbs interactions between the yeast FACT (yFACT) complex and chromatin during transcription, resulting in a pronounced shift in yFACT occupancy toward the 3′ ends of transcribed genes. In the present study we report that two histone H4 mutants—H4-R36A and H4-K31E—alter the association pattern of the yFACT subunit Spt16 across transcribed genes in a fashion similar to that seen for H3-L61W. Interestingly, H4-R36, H4-K31, and H3-L61 are in close proximity to each other on the side of the nucleosome. We also provide evidence that the H4-R36A and H3-L61W mutants impair proper Spt16−chromatin interactions by perturbing a common process. Collectively, our results suggest that a nucleosomal region encompassing the H4-R36, H4-K31, and H3-L61 residues plays an important role in ensuring proper association of yFACT across transcribed genes.
Biodiversity effects of ecosystem engineers are stronger on more complex ecosystem processes
Authors: Caliman Adriano , Carneiro Luciana S. , Leal João J. F. , Farjalla Vinicius F. , Bozelli Reinaldo L. , Esteves Francisco A.
Published: April 2013

The relative importance of species richness and identity for the diversity–function relationship remains controversial. We mechanistically explored the potential contribution of ecosystem processes complexity (EPC; i.e., the number of pathways and mechanisms through which an ecosystem process can be directly and/or indirectly affected by species and/or their interactions) to the resolution of this controversy. We hypothesized that the complementarity effects of biodiversity will be stronger and that the diversity–function relationship will be more dependent on species richness as the EPC increases. Using a benthic bioturbator community as a model system we tested these predictions across ecosystem processes that could be ordered according to their complexity (suspended material flux < PO4‐P flux < NH4‐N flux < bacterioplankton production). Consistent with our predictions, species richness explained an increasing proportion of data variation as EPC increased, whereas the contrary was observed for species composition. Nontransgressive overyielding was not affected by EPC, but the magnitude of transgressive overyielding increased significantly with EPC, indicating that complementarity may be stronger as EPC increases. Our results highlight the importance of considering the interactive role of the characteristics of ecosystem processes in our theoretical understanding of the diversity–function relationship and its underlying mechanisms.
Stochastic processes dominate during boreal bryophyte community assembly
Authors: Fenton Nicole J. , Bergeron Yves
Published: April 2013

Why are plant species found in certain locations and not in others? The study of community assembly rules has attempted to answer this question, and many studies articulate the historic dichotomy of deterministic (predictable niches) vs. stochastic (random or semi‐random processes). The study of successional sequences to determine whether they converge, as would be expected by deterministic theory, or diverge, as stochastic theory would suggest, has been one method used to investigate this question. In this article we ask the question: Do similar boreal bryophyte communities develop in the similar habitat created by convergent succession after fires of different severities? Or do the stochastic processes generated by fires of different severity lead to different communities? Specifically we predict that deterministic structure will be more important for large forest‐floor species than stochastic processes, and that the inverse will be true for small bryophyte species. We used multivariate regression trees and model selection to determine the relative weight of structure (forest structure, substrates, soil structure) and processes (fire severity) for two groups of bryophyte species sampled in 12 sites (seven high‐severity and five low‐severity fires). Contrary to our first hypothesis, processes were as important for large forest‐floor bryophytes as for small pocket species. Fire severity, its interaction with the quality of available habitat, and its impact on the creation of biological legacies played dominant roles in determining community structure. In this study, sites with nearly identical forest structure, generated via convergent succession after high‐ and low‐severity fire, were compared to see whether these sites supported similar bryophyte communities. While similar to some degree, both the large forest‐floor species and the pocket species differed after high‐severity fire compared to low‐severity fire. This result suggests that the “how,” or process of habitat generation, influences community composition in this system and that a snapshot of habitat conditions taken at only one point in time is insufficient to explain species distribution.
The Decision‐Making Process for Ridge Preservation Procedures After Tooth Extraction
Authors: Frost Natalie A. , Banjar Arwa A. , Galloway Patrick B. , Huynh‐Ba Guy , Mealey Brian L.
Published: April 2013

Focused Clinical Question:How should the extraction socket be managed after tooth removal?

Summary:Resorptive changes that take place after tooth extraction can result in a significant reduction in alveolar ridge width and height. This may create a problem for proper implant placement and fabrication of esthetic restorations. Ridge preservation has been shown to be effective in decreasing alveolar bone resorption after tooth removal. During ridge preservation, the extraction socket is filled with graft material, and a barrier is generally used to contain the graft. Flap reflection is usually not recommended if the socket walls are intact and the ridge width is sufficient after tooth removal. However, if significant breakdown of the buccal bony plate is present, mucoperiosteal flap elevation may be required to allow proper placement of the bone graft and membrane. Different types of bone grafts (autograft, allograft, and xenograft) and barrier membranes (resorbable and non‐resorbable) have been evaluated in clinical studies. They all are shown to be effective regardless of the material or technique used.

Conclusions:Ridge preservation is an effective procedure for minimizing horizontal and vertical alveolar ridge resorption after tooth extraction. Current evidence does not support one technique as being superior to another. The selection of the technique to be used should be based on the clinical situation.
Application of commercial poly(3,4-ethylenedioxy-thiophene):poly(styrene sulfonate) for electrochemical sensing of dopamine
Authors: Yao Yuanyuan , Wen Yangping , Xu Jingkun , Zhang Long , Duan Xuemin
Published: April 2013

In this paper, a simple and stable composite electrode based on intrinsically
conducting polymer poly(3,4-ethylenedioxythiophene):poly(sty-renesulfonate)
(PEDOT:PSS) and ion-exchange polymer Nafion, was successfully fabricated by
drop-coating the blended commercially available PEDOT:PSS aqueous dispersion
and Nafion solution on the surface of glassy carbon electrode (GCE).
PEDOT:PSS was used as a matrix, while Nafion was employed to improve the
immobilization stability of composite films and adhesion to electrode surface
in comparison with PEDOT:PSS films. Cyclic voltammetry, differential pulse
voltammetry, electrochemical impedance spectroscopy, and scanning electron
microscopy were utilized to characterize the properties of this composite
electrode. The as-proposed composite electrode displayed good
water-stability. Meanwhile, the composite electrode was applied to
electrochemical sensing of dopamine, and the performance of PEDOT:PSS-Nafion
composite films was evaluated. These results demonstrate that
PEDOT:PSS-Nafion composites are a promising candidate of electrode modified
material in electrochemical sensing and other electrocatalytic applications.
Lattice Boltzmann simulation of melting phenomenon with natural convection from an eccentric annulus
Authors: Jourabian Mahmoud , Farhadi Mousa , Rabienataj Darzi , Abouei Abbas
Published: April 2013

In the present study, a double-population thermal lattice Boltzmann was
applied to solve phase change problem with natural convection in an eccentric
annulus. The simulation of melting process from a concentrically and
eccentrically placed inner hot cylinder inside an outer cold cylinder with
Prandtl number of 6.2, Stefan number of 1 and Rayleigh number of 105 was
carried out quantitatively. It was found that the position of the inner
cylinder inside the outer cylinder significantly influence the flow patterns
including the size and shape of two formed vortexes. It is also observed that
the maximum of liquid fractions occurs where the inner cylinder is mounted at
the bottom of outer cylinder.
The composition of gaseous products from corn stalk pyrolysis process
Authors: Djuric Slavko , Brankov Sasa , Kosanic Tijana , Ceranic Mirjana , Nakomcic-Smaragdakis Branka
Published: April 2013

This paper describes experimental investigation of corn stalk pyrolysis. The
mass of the sample (corn stalk) inside a pyrolytic reactor was 10 g with
particle diameter of 5-10 mm. The sample in the reactor was heated in the
temperature range of 24-650?C and the gas components generated during corn
stalk pyrolysis were measured using gas analyzer G750 POLYTECTOR II. The
sample mass before, during and after pyrolysis process was determined by
using METTLER P1000 digital scale. Experimental results of the corn stalk
pyrolysis indicate that as the temperature in the reactor increases from
300-650?C, the pyrolytic gas yield increases from 60-72%, while the char
(coke) yield decreases from 40-28%. In the temperature range mentioned, the
CO2 volume fraction in pyrolytic gas decreases, while the volume fraction of
methane increases up to 39.5% followed with a constant decrease in the volume
fraction of oxygen. The results obtained can represent starting basis for
determining material and heat balance of pyrolysis process as well as corn
stalk pyrolysis equipment.
The determination of optimum injection pressure in an engine fuelled with soybean biodiesel/diesel blend
Authors: Çelik Bahattin , Şimşek Doğan
Published: April 2013

In this study, the optimum blend rate and injection pressure in a
four-stroke, single cylinder, direct injection diesel engine using soybean
methyl ester were investigated experimentally. The tests were conducted at
two stages. Firstly, the engine was tested with diesel fuel, B25 (25%
biodiesel+75% diesel fuel), B50, B75 and B100 fuels at full load and at a
constant speed. According to the test results, it was determined that the
most suitable fuel was B25 in terms of performance and emission. Secondly,
the engine was tested at different loads with diesel fuel at original
injection pressure and with B25 at different injection pressures (160, 180,
200, 220, 240 bar) for comparison. It was determined from tests performed
with B25 that the most suitable injection pressure in terms of performance
and emissions was 220 bar. The specific fuel consumption and power values of
the B25 were found to be nearly the same as those of diesel fuel at 220 bar
injection pressure. In addition, HC, CO, and smoke emissions were reduced by
about 33%, 9% and 20%, respectively. On the other hand, NOx emission
increased by about 12%.
Ramm Wholesale: Reviewing Audit Work (Retracted)
Authors: Kalesnikoff Douglas , Phillips Fred
Published: April 2013

Designed to be used in an undergraduate or Master's auditing course, this Case asks students to evaluate work performed on the financial statement audit of a private wholesale merchandiser. Through this evaluation, students can uncover issues relating to gaining knowledge of a client and its environment, risk assessment, materiality, audit strategy, and specific audit procedures for the revenue/receivables/receipts accounting cycle. The Teaching Notes provide support both for instructors who ask students to prepare the Case in advance of class and for instructors who instead assign the Case for analysis in real-time during class, whereby the Case is read aloud paragraph-by-paragraph and issues are discussed as they are detected.
Role of polyaniline morphology in Pd particles dispersion. Hydrogenation of alkynes in the presence of Pd-polyaniline catalysts
Authors: Kosydar Robert , Goral Monika , Drelinkiewicz Alicja , Stejskal Jaroslav
Published: April 2013

Two polyaniline (PANI) samples of various molecular masses were used for the preparation of palladium catalysts (with 2 mass % of Pd). The physicochemical features of starting polyanilines were found to substantially affect the size and extent of palladium nanoparticles aggregation. Strongly aggregated large palladium particles appeared in the PANI sample of more compact morphology (PANI-H), higher crystallinity and lower specific surface area. Pd nanoparticles of a definitively smaller size were formed in the more amorphous PANI sample of looser morphology (PANI-L) and the extent of particles aggregation was markedly lower. The catalytic properties of Pd/PANI samples were studied in a liquid phase hydrogenation of unsaturated triple bond (C≡C) in alkynes reactants, phenylacetylene, and cyclohexylacetylene. The 2 mass % Pd/PANI-L catalyst prepared using polymer of less compact texture exhibited much higher activity in both reactions. In the presence of the 2 mass % Pd/PANI-L catalyst, alkene products were formed with a high selectivity (approximately 90 %) attained at the almost complete conversion of alkynes. This highly selective hydrogenation of the C≡C to the C=C bond was related to the presence of an electroactive polymer, PANI, in close proximity with Pd active sites. Polyaniline could have a role in a steric effect as well as in a modification of adsorptive properties of Pd centres.
CFD-based atmospheric dispersion modeling in real urban environments
Authors: Labovský Juraj , Jelemenský Ľudovít
Published: April 2013

The process of CFD model application for atmospheric dispersion modeling is presented. Increasing the CPU power opens new possibilities of the CFD approach application for consequence analysis in real complex urban environments. As successful CFD simulation is directly dependent on the quality and complexity of the computational mesh, a new methodology of transferring the Geographic Information System (GIS) data to the computational mesh can be utilized. A user software for importing and manipulation with the GIS data and their subsequent transfer to an instructional file for the generation of the computational mesh was prepared and tested. The introduced methodology is relatively simple and it requires only a small amount of input data. The process of creating a computational mesh is very straightforward and fast, which enables the application of CFD modeling in urban environments in all fields of engineering applications in safety analysis. Several recommendations concerning proper definition of boundary conditions for atmospheric dispersion modeling were summarized. The presented approach was tested on a realistic case study of liquefied chlorine release in a real town. Results obtained by the CFD approach were compared with those obtained by a simpler but standard integral model.
The Turd in the Rath: Antiquarians, the Ordnance Survey, and Beckett's Irish Landscapes
Authors: Parsons Cóilín
Published: April 2013

This paper engages with one of the potential sources to which the experience of being lost, or misrecognising the landscape, that is so common in Beckett's work might be traced. Linking Beckett's often ignored early collection of short stories, More Pricks Than Kicks, to the abstract landscapes of the post-war fiction, allows us to trace an interest in unsettled places to a much earlier point in Beckett's work than is usually allowed. The interest in antiquities so prevalent in the early fiction emerges from a larger national conversation in Ireland about the preservation of the Gaelic past in the face of capital's push for abstract space. This work of preservation was begun by the Ordnance Survey in the 1830s, and the Survey's abstract representations of a landscape fractured by colonialism bears many resemblances to Beckett's early landscapes, which this paper traces. The tendency towards placelessness was already a key component of Beckett's most placed early work – he recognised that the landscape of Ireland was radically alienated from itself.
A Program for Solving the Brain Ischemia Problem
Authors: DeGracia Donald
Published: April 2013

Our recently described nonlinear dynamical model of cell injury is here applied to the problems of brain ischemia and neuroprotection. We discuss measurement of global brain ischemia injury dynamics by time course analysis. Solutions to proposed experiments are simulated using hypothetical values for the model parameters. The solutions solve the global brain ischemia problem in terms of “master bifurcation diagrams” that show all possible outcomes for arbitrary durations of all lethal cerebral blood flow (CBF) decrements. The global ischemia master bifurcation diagrams: (1) can map to a single focal ischemia insult, and (2) reveal all CBF decrements susceptible to neuroprotection. We simulate measuring a neuroprotectant by time course analysis, which revealed emergent nonlinear effects that set dynamical limits on neuroprotection. Using over-simplified stroke geometry, we calculate a theoretical maximum protection of approximately 50% recovery. We also calculate what is likely to be obtained in practice and obtain 38% recovery; a number close to that often reported in the literature. The hypothetical examples studied here illustrate the use of the nonlinear cell injury model as a fresh avenue of approach that has the potential, not only to solve the brain ischemia problem, but also to advance the technology of neuroprotection.
Characterization of Active Sites/Entities and Redox/Catalytic Correlations in Copper-Ceria-Based Catalysts for Preferential Oxidation of CO in H2-Rich Streams
Authors: Martínez-Arias Arturo , Gamarra Daniel , Hungría Ana , Fernández-García Marcos , Munuera Guillermo , Hornés Aitor , Bera Parthasarathi , Conesa José , Cámara Antonio
Published: April 2013

This article reviews work done at authors’ laboratories about catalysts based on combinations between copper and ceria for preferential oxidation of CO in H2-rich streams (CO-PROX). The main focus of this review is the characterization of active sites for the process on the basis of spectroscopic analysis of the systems under reaction conditions (operando techniques). On such a basis, it is exposed the state of the art in this field in connection with results obtained in other laboratories.
Molecular Dynamics Simulations on Evaporation of Droplets with Dissolved Salts
Authors: Wang Bing-Bing , Wang Xiao-Dong , Chen Min , Xu Jin-Liang
Published: April 2013

Molecular dynamics simulations are used to study the evaporation of water droplets containing either dissolved LiCl, NaCl or KCl salt in a gaseous surrounding (nitrogen) with a constant high temperature of 600 K. The initial droplet has 298 K temperature and contains 1,120 water molecules, 0, 40, 80 or 120 salt molecules. The effects of the salt type and concentration on the evaporation rate are examined. Three stages with different evaporation rates are observed for all cases. In the initial stage of evaporation, the droplet evaporates slowly due to low droplet temperature and high evaporation latent heat for water, and pure water and aqueous solution have almost the same evaporation rates. In the second stage, evaporation rate is increased significantly, and evaporation is somewhat slower for the aqueous salt-containing droplet than the pure water droplet due to the attracted ion-water interaction and hydration effect. The Li+-water has the strongest interaction and hydration effect, so LiCl aqueous droplets evaporate the slowest, then NaCl and KCl. Higher salt concentration also enhances the ion-water interaction and hydration effect, and hence corresponds to a slower evaporation. In the last stage of evaporation, only a small amount of water molecules are left in the droplet, leading to a significant increase in ion-water interactions, so that the evaporation becomes slower compared to that in the second stage.
A New State of Charge Estimation Method for LiFePO4 Battery Packs Used in Robots
Authors: Chang Ming-Hui , Huang Han-Pang , Chang Shu-Wei
Published: April 2013

The accurate state of charge (SOC) estimation of the LiFePO4 battery packs used in robot applications is required for better battery life cycle, performance, reliability, and economic issues. In this paper, a new SOC estimation method, “Modified ECE + EKF”, is proposed. The method is the combination of the modified Equivalent Coulombic Efficiency (ECE) method and the Extended Kalman Filter (EKF) method. It is based on the zero-state hysteresis battery model, and adopts the EKF method to correct the initial value used in the Ah counting method. Experimental results show that the proposed technique is superior to the traditional techniques, such as ECE + EKF and ECE + Unscented Kalman Filter (UKF), and the accuracy of estimation is within 1%.
Expression, Purification and Identification of CtCVNH, a Novel Anti-HIV (Human Immunodeficiency Virus) Protein from Ceratopteris thalictroides
Authors: Sun Junbo , Su Yingjuan , Wang Ting
Published: April 2013

CVN (cyanovirin-N) is an anti-HIV protein. CVNH (cyanovirin-N homology) represents its homology. In a previous study, we first reported the full-length sequences of the CVNH gene cloned from Ceratopteris thalictroides. Based on the finding, the coding sequence of CtCVNH was optimized in the study, and then a pET prokaryotic expression vector was constructed. The purification and identification of CtCVNH protein were investigated, as well. SDS-PAGE analysis indicated that a 31 kDa protein was overexpressed and mainly accumulated in the soluble fraction. Only a single protein was obtained after the Ni- nitrilotriacetic acid (NTA) affinity chromatography. The purified protein was identified to be the recombinant CtCVNH by both Western blot and peptide mass fingerprinting analysis.
Quantification of Maternal Serum Cell-Free Fetal DNA in Early-Onset Preeclampsia
Authors: Yu Hong , Shen Yanting , Ge Qinyu , He Youji , Qiao Dongyan , Ren Mulan , Zhang Jianqiong
Published: April 2013

The aim of this study was to determine whether the increased serum cell-free fetal DNA (cffDNA) level of gravidas developed into early-onset preeclampsia (EOPE) subsequently in the early second trimesters is related to prenatal screening markers. Serum was collected from 1011 gravidas. The level of cffDNA and prenatal screening markers were analyzed in 20 cases with EOPE and 20 controls. All fetuses were male. The maternal serum cffDNA level was assessed by ampliﬁcation of the Y chromosome speciﬁc gene. Correlations between the variables were examined. (Logged) cffDNA in EOPE (median, 3.08; interquartile range, 2.93–3.68) was higher than controls (median, 1.79; interquartile range, 1.46–2.53). The increased level of (logged) cffDNA was correlated signiﬁcantly with the increased human chorionic gonadotropin (HCG) level (r = 0.628, p < 0.001). Significant reciprocal correlations between cffDNA and babies’ birth weight as well as gestation weeks at delivery were noted (r = −0.516, p = 0.001; r = −0.623, p < 0.001, respectively). The sensitivity and speciﬁcity of cffDNA to discriminate between the EOPE cases and the controls were 90% and 85%, respectively. CffDNA is a potential marker for EOPE, which had a significant reciprocal correlation with babies’ birth weight and gestation weeks at delivery. Moreover, it may help in indicating the underlying hypoxic condition in the placenta.
Multiple Sclerosis: From Molecules to Treatment
Authors: Broadley Simon
Published: April 2013

The treatment of multiple sclerosis has been radically transformed over the past 20 years and this special issue of IJMS, focusing on the molecular aspects of the disease, highlights the growing conformity of the various investigative approaches. It is a very exciting time to be involved in the research of this disease.
Melatonin Inhibits GnRH-1, GnRH-3 and GnRH Receptor Expression in the Brain of the European Sea Bass, Dicentrarchus labrax
Authors: Servili Arianna , Herrera-Pérez Patricia , Del Carmen Rendón María , Muñoz-Cueto José
Published: April 2013

Several evidences supported the existence of melatonin effects on reproductive system in fish. In order to investigate whether melatonin is involved in the modulation of GnRH systems in the European sea bass, we have injected melatonin (0.5 µg/g body mass) in male specimens. The brain mRNA transcript levels of the three GnRH forms and the five GnRH receptors present in this species were determined by real time quantitative PCR. Our findings revealed day–night variations in the brain expression of GnRH-1, GnRH-3 and several GnRH receptors (dlGnRHR-II-1c, -2a), which exhibited higher transcript levels at mid-light compared to mid-dark phase of the photocycle. Moreover, an inhibitory effect of melatonin on the nocturnal expression of GnRH-1, GnRH-3, and GnRH receptors subtypes 1c, 2a and 2b was also demonstrated. Interestingly, the inhibitory effect of melatonin affected the expression of hypophysiotrophic GnRH forms and GnRH receptors that exhibit day–night fluctuations, suggesting that exogenous melatonin reinforce physiological mechanisms already established. These interactions between melatoninergic and GnRH systems could be mediating photoperiod effects on reproductive and other rhythmic physiological events in the European sea bass.
Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses
Authors: Hahn Achim , Kilian Joachim , Mohrholz Anne , Ladwig Friederike , Peschke Florian , Dautel Rebecca , Harter Klaus , Berendzen Kenneth , Wanke Dierk
Published: April 2013

Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmotic and salt) can be examined for their capacity to generate systemic signals between the shoot and root, which might be essential to regain homeostasis in Arabidopsis thaliana. We classified the systemic responses into two groups: genes that are regulated in the non-treated tissue only are defined as type I responsive and, accordingly, genes that react in both tissues are termed type II responsive. Analysis of type I and II systemic responses suggest distinct functionalities, but also significant overlap between different stresses. Comparison with salicylic acid (SA) and methyl-jasmonate (MeJA) responsive genes implies that MeJA is involved in the systemic stress response. Certain genes are predominantly responding in only one of the categories, e.g., WRKY genes respond mainly non-systemically. Instead, genes of the plant core environmental stress response (PCESR), e.g., ZAT10, ZAT12, ERD9 or MES9, are part of different response types. Moreover, several PCESR genes switch between the categories in a stress-specific manner.
Gene Cloning, Expression and Characterization of a Novel Xylanase from the Marine Bacterium, Glaciecola mesophila KMM241
Authors: Guo Bing , Li Ping-Yi , Yue Yong-Sheng , Zhao Hui-Lin , Dong Sheng , Song Xiao-Yan , Sun Cai-Yun , Zhang Wei-Xin , Chen Xiu-Lan , Zhang Xi-Ying , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: April 2013

Marine xylanases are rather less studied compared to terrestrial xylanases. In this study, a new xylanase gene, xynB, was cloned from the marine bacterium, Glaciecola mesophila KMM241, and expressed in Escherichia coli. xynB encodes a multi-domain xylanase XynB of glycoside hydrolase (GH) family 8. The recombinant XynB comprises an N-terminal domain (NTD) with unknown function and a catalytic domain, which is structurally novel among the characterized xylanases of GH family 8. XynB has the highest identity (38%) to rXyn8 among the characterized xylanases. The recombinant XynB showed maximal activity at pH 6–7 and 35 °C. It is thermolabile and salt-tolerant. XynB is an endo-xylanase that demands at least five sugar moieties for effective cleavage and to hydrolyze xylohexaose and xylopentaose into xylotetraose, xylotriose and xylobiose. NTD was expressed in Escherichia coli to analyze its function. The recombinant NTD exhibited a high binding ability to insoluble xylan and avicel and little binding ability to chitosan and chitin. Since the NTD shows no obvious homology to any known carbohydrate-binding module (CBM) sequence in public databases, XynB may contain a new type of CBM.
Protostane and Fusidane Triterpenes: A Mini-Review
Authors: Zhao Ming , Gödecke Tanja , Gunn Jordan , Duan Jin-Ao , Che Chun-Tao
Published: April 2013

Protostane triterpenes belong to a group of tetracyclic triterpene that exhibit unique structural characteristics. Their natural distribution is primarily limited to the genus Alisma of the Alismataceae family, but they have also been occasionally found in other plant genera such as Lobelia, Garcinia, and Leucas. To date, there are 59 known protostane structures. Many of them have been reported to possess biological properties such as improving lipotropism, hepatoprotection, anti-viral activity against hepatitis B and HIV-I virus, anti-cancer activity, as well as reversal of multidrug resistance in cancer cells. On the other hand, fusidanes are fungal products characterized by 29-nor protostane structures. They possess antibiotic properties against staphylococci, including the methicillin-resistant Staphylococcus aureus (MRSA). Fusidic acid is a representative member which has found clinical applications. This review covers plant sources of the protostanes, their structure elucidation, characteristic structural and spectral properties, as well as biological activities. The fungal sources, structural features, biological activities of fusidanes are also covered in this review. Additionally, the biogenesis of these two types of triterpenes is discussed and a refined pathway is proposed.
Is Selenium a Potential Treatment for Cancer Metastasis?
Authors: Chen Yu-Chi , Prabhu K. , Mastro Andrea
Published: April 2013

Selenium (Se) is an essential micronutrient that functions as a redox gatekeeper through its incorporation into proteins to alleviate oxidative stress in cells. Although the epidemiological data are somewhat controversial, the results of many studies suggest that inorganic and organic forms of Se negatively affect cancer progression, and that several selenoproteins, such as GPXs, also play important roles in tumor development. Recently, a few scientists have examined the relationship between Se and metastasis, a late event in cancer progression, and have evaluated the potential of Se as an anti-angiogenesis or anti-metastasis agent. In this review, we present the current knowledge about Se compounds and selenoproteins, and their effects on the development of metastasis, with an emphasis on cell migration, invasion, and angiogenesis. In the cancers of breast, prostate, colorectal, fibrosarcoma, melanoma, liver, lung, oral squamous cell carcinoma, and brain glioma, there is either clinical evidence linking selenoproteins, such as thioredoxin reductase-1 to lymph node metastasis; in vitro studies indicating that Se compounds and selenoproteins inhibited cell motility, migration, and invasion, and reduced angiogenic factors in some of these cancer cells; or animal studies showing that Se supplementation resulted in reduced microvessel density and metastasis. Together, these data support the notion that Se may be an anti-metastastatic element in addition to being a cancer preventative agent.
Localization and Mapping Using Only a Rotating FMCW Radar Sensor
Authors: Vivet Damien , Checchin Paul , Chapuis Roland
Published: April 2013

Rotating radar sensors are perception systems rarely used in mobile robotics. This paper is concerned with the use of a mobile ground-based panoramic radar sensor which is able to deliver both distance and velocity of multiple targets in its surrounding. The consequence of using such a sensor in high speed robotics is the appearance of both geometric and Doppler velocity distortions in the collected data. These effects are, in the majority of studies, ignored or considered as noise and then corrected based on proprioceptive sensors or localization systems. Our purpose is to study and use data distortion and Doppler effect as sources of information in order to estimate the vehicle’s displacement. The linear and angular velocities of the mobile robot are estimated by analyzing the distortion of the measurements provided by the panoramic Frequency Modulated Continuous Wave (FMCW) radar, called IMPALA. Without the use of any proprioceptive sensor, these estimates are then used to build the trajectory of the vehicle and the radar map of outdoor environments. In this paper, radar-only localization and mapping results are presented for a ground vehicle moving at high speed.
Optical System Error Analysis and Calibration Method of High-Accuracy Star Trackers
Authors: Sun Ting , Xing Fei , You Zheng
Published: April 2013

The star tracker is a high-accuracy attitude measurement device widely used in spacecraft. Its performance depends largely on the precision of the optical system parameters. Therefore, the analysis of the optical system parameter errors and a precise calibration model are crucial to the accuracy of the star tracker. Research in this field is relatively lacking a systematic and universal analysis up to now. This paper proposes in detail an approach for the synthetic error analysis of the star tracker, without the complicated theoretical derivation. This approach can determine the error propagation relationship of the star tracker, and can build intuitively and systematically an error model. The analysis results can be used as a foundation and a guide for the optical design, calibration, and compensation of the star tracker. A calibration experiment is designed and conducted. Excellent calibration results are achieved based on the calibration model. To summarize, the error analysis approach and the calibration method are proved to be adequate and precise, and could provide an important guarantee for the design, manufacture, and measurement of high-accuracy star trackers.
Toward One Giga Frames per Second — Evolution of in Situ Storage Image Sensors
Authors: Etoh Takeharu , Son Dao , Yamada Tetsuo , Charbon Edoardo
Published: April 2013

The ISIS is an ultra-fast image sensor with in-pixel storage. The evolution of the ISIS in the past and in the near future is reviewed and forecasted. To cover the storage area with a light shield, the conventional frontside illuminated ISIS has a limited fill factor. To achieve higher sensitivity, a BSI ISIS was developed. To avoid direct intrusion of light and migration of signal electrons to the storage area on the frontside, a cross-sectional sensor structure with thick pnpn layers was developed, and named “Tetratified structure”. By folding and looping in-pixel storage CCDs, an image signal accumulation sensor, ISAS, is proposed. The ISAS has a new function, the in-pixel signal accumulation, in addition to the ultra-high-speed imaging. To achieve much higher frame rate, a multi-collection-gate (MCG) BSI image sensor architecture is proposed. The photoreceptive area forms a honeycomb-like shape. Performance of a hexagonal CCD-type MCG BSI sensor is examined by simulations. The highest frame rate is theoretically more than 1Gfps. For the near future, a stacked hybrid CCD/CMOS MCG image sensor seems most promising. The associated problems are discussed. A fine TSV process is the key technology to realize the structure.
Analyzing Migratory Properties of Human CD133+ Stem Cells in Vivo after Intraoperative Sternal Bone Marrow Isolation
Authors: Donndorf Peter , Useini Dritan , Lux Cornelia A. , Vollmar Brigitte , Delyagina Evgenya , Laupheimer Michael , Kaminski Alexander , Steinhoff Gustav
Published: April 2013

Human bone marrow stem cell populations have been applied for cardiac regeneration purposes within different clinical settings in the recent past. The migratory capacity of applied stem cell populations towards injured tissue, after undergoing specific peri-interventional harvesting and isolation procedures, represents a key factor limiting therapeutic efficacy. We therefore aimed at analyzing the migratory capacity of human cluster of differentiation (CD) 133+ bone marrow stem cells in vivo after intraoperative harvesting from the sternal bone marrow. Human CD133+ bone marrow stem cells were isolated from the sternal bone marrow of patients undergoing cardiac surgery at our institution. Migratory capacity towards stromal cell-derived factor-1α (SDF-1α) gradients was tested in vitro and in vivo by intravital fluoresecence microscopy, utilizing the cremaster muscle model in severe combined immunodeficient (SCID) mice and analyzing CD133+ cell interaction with the local endothelium. Furthermore, the role of a local inflammatory stimulus for CD133+ cell interaction with the endothelium was studied. In order to describe endothelial response upon chemokine stimulation laser scanning microscopy of histological cremaster muscle samples was performed. SDF-1α alone was capable to induce relevant early CD133+ cell interaction with the endothelium, indicated by the percentage of rolling CD133+ cells (45.9 ± 1.8% in “SDF-1” vs. 17.7 ± 2.7% in “control,” p < 0.001) and the significantly reduced rolling velocity after SDF-1α treatment. Furthermore, SDF-1α induced firm endothelial adhesion of CD133+ cells in vivo. Firm endothelial adhesion, however, was significantly enhanced by additional inflammatory stimulation with tumor necrosis factor-α (TNF-α) (27.9 ± 4.3 cells/mm2 in “SDF-1 + TNF” vs. 2.2 ± 1.1 cells/mm2 in “control,” p < 0.001). CD133+ bone marrow stem cells exhibit sufficient in vivo homing towards SDF-1α gradients in an inflammatory microenvironment after undergoing standardized intraoperative harvesting and isolation from the sternal bone marrow.
Amelioration of Paraquat-Induced Pulmonary Injury by Mesenchymal Stem Cells
Authors: Tsai Hsin-Lin , Chang Jei-Wen , Yang Hui-Wen , Chen Chang-Wei , Yang Chen-Chang , Yang An-Hang , Liu Chin-Su , Chin Tai-Wai , Wei Chou-Fu , Lee Oscar K.
Published: April 2013

Acute paraquat (PQ) poisoning induces redox cycle and leads to fatal injury of lung. Clinical management is supportive in nature due to lack of effective antidote, and the mortality is very high. Mesenchymal stem cells (MSCs) process the properties of immunomodulation, anti-inflammatory, and antifibrotic effects and oxidative stress resistance. MSC transplantation may theoretically serve as an antidote in PQ intoxication. In this study, we examined the potential therapeutic effects of MSCs in PQ-induced lung injury. The degree of PQ toxicity in the rat type II pneumocyte cell line, L2, and MSCs was evaluated by examining cell viability, ultrastructural changes, and gene expression. L2 cells treated with 0.5 mM PQ were cocultured in the absence or presence of MSCs. For the in vivo study, adult male SD rats were administered an intraperitoneal injection of PQ (24 mg/kg body weight) and were divided into three groups: group I, control; group II, cyclophosphamide and methylprednisolone; group III, MSC transplantation 6 h after PQ exposure. MSCs were relatively resistant to PQ toxicity. Coculture with MSCs significantly inhibited PQ accumulation in L2 cells and upregulated the expression of antioxidative heme oxygenase 1 and metallothionein 1a genes, reversed epithelial-to-mesenchymal transition, and increased the viability of PQ-exposed L2 cells. Treatment with MSCs resulted in a significant reduction in severity of liver and renal function deterioration, alleviated lung injury, and prolonged the life span of rats. Altogether, our results suggest that MSCs possess antidote-like effect through multifactorial protection mechanism. The results of this preclinical study demonstrate that transplantation of MSCs may be a promising therapy and should be further validated clinically.
La jerarquía católica española en perspectiva comparada. La confrontación política entre la Iglesia y el Gobierno socialista a comienzos del siglo XXI
Authors: Aguilar Susana
Published: April 2013

La Iglesia católica española (ICE) constituye un grupo de interés multi-issue con distintos resultados en su actividad política: la financiación y la educación son asuntos clave en los que está protegida por los Acuerdos de 1979, pero los poderes públicos no tienen la obligación de negociar con esta institución políticas de contenido moral. Como respuesta a la liberalización del aborto y a la aprobación del matrimonio de personas del mismo sexo, promovidas por el Gobierno de Rodríguez Zapatero, la ICE, a diferencia de otras instituciones eclesiásticas en Europa en situaciones parecidas, desarrolla una estrategia de confrontación junto con grupos católicos conservadores y, en menor medida, partidos políticos afines. Su posición “monopolista” en una sociedad que se define mayoritariamente como católica (argumento sociológico), la inextricable imbricación entre catolicismo e identidad nacional (argumento histórico), y su privilegiada relación con el Estado, que deriva de los Acuerdos de 1979 y del aconfesionalismo constitucional (argumento institucional), pueden explicar esta estrategia. Mientras que la Conferencia Episcopal (CE) es la principal responsable de la confrontación a nivel estatal, los obispos, a nivel autonómico, se han aprestado a través de un gran número de convenios con las autoridades regionales a defender los intereses de la Iglesia y minimizar los posibles “daños” que derivan del ámbito estatal. El Estado autonómico ha multiplicado los puntos de acceso al sistema político para la Iglesia y podría suceder que la CE terminara perdiendo peso político a favor de las conferencias episcopales regionales, promovidas no solo por las iglesias periféricas nacionalistas sino, también, por la creciente relevancia del nivel autonómico frente al estatal para los intereses eclesiásticos.
Applying Continuous Authentication to Protect Electronic Transactions
Authors: Albuquerque Silas Leite , Gondim Paulo Roberto de Lira
Published: April 2013

In this sense, this chapter explores some possibilities for continuous authentication use to increase electronic transactions security and addresses issues such: Trust in electronic communications systems, conventional authentication models, continuous authentication concepts and biometrics.