bluuebunny/crossref_metadata_2025 huggingface dataset:
Crosstalk between the urokinase-type plasminogen activator receptor and EGF receptor variant III supports survival and growth of glioblastoma cells
Authors: Hu Jingjing , Jo Minji , Cavenee Webster K. , Furnari Frank , VandenBerg Scott R. , Gonias Steven L.
Published: September 2011

A truncated and constitutively active form of the EGF receptor, variant III (EGFRvIII), is a major determinant of tumor growth and progression in glioblastoma multiforme (GBM). Extensive bidirectional crosstalk occurs in the cell-signaling pathways downstream of the EGFR and the urokinase-type plasminogen activator receptor (uPAR); however, crosstalk between EGFRvIII and uPAR has not been examined. Here, we show that uPAR does not regulate ERK activation in EGFRvIII-expressing GBM cells; however, in GBM cells isolated from four separate xenografts in which EGFRvIII expression was down-regulated in vivo, uPAR assumed a major role in sustaining ERK activation. Phosphorylation of Tyr-845 in the EGFR, which is mediated by Src family kinases, depended on uPAR in EGFRvIII-expressing GBM cells. Activation of the mitogenic and prosurvival transcription factor, STAT5b, downstream of EGFRvIII, also required uPAR. The EGFR-selective tyrosine kinase inhibitors, erlotinib and gefitinib, blocked not only EGFRvIII signaling to ERK but also uPAR-dependent STAT5b activation. uPAR gene silencing in EGFRvIII-expressing GBM cells and in cells from tumors that escaped dependency on EGFRvIII decreased cell survival and proliferation. Xenografts of EGFRvIII-expressing cancer cell lines and a human GBM, which was propagated as a xenograft, were robustly immunopositive for uPAR and phospho–Tyr-845 by immunohistochemistry. A human GBM in which the EGFR gene was amplified without truncation was immunonegative for both uPAR and phospho–Tyr-845. These studies identify distinct cell-signaling activities for uPAR in GBM cells that express EGFRvIII and in cells released from dormancy when EGFRvIII is neutralized. uPAR and its crosstalk pathways with EGFRvIII emerge as logical targets for therapeutics development in GBM.
Influence of Multiple-Day Temporal Distribution of Repetitions on Memory: A Comparison of Uniform, Expanding, and Contracting Schedules
Authors: Gerbier Emilie , Koenig Olivier
Published: September 2011

Very few studies have examined the influence of schedules of repetitions across multiple days (e.g., Tsai, 1927). Three temporal schedules of four presentations of pseudoword/word pairs over a 7-day learning period were compared: a uniform (presentations on Days 1, 3, 5, and 7), an expanding (1, 2, 3, 7), and a contracting (1, 5, 6, 7) schedule. Schedule was a within-subjects variable. Experiment 1 was performed on the Internet and showed that cued recall on Day 9 led to higher scores for the stimuli of the expanding schedule. Experiment 2 was performed in the laboratory and showed that the expanding and the uniform schedules led to the highest scores on Day 9. A recognition task performed during the learning phase revealed that stimuli recognized at the time of their repetition were more likely to be retrieved later than the others. Our results are discussed within the framework of the study-phase retrieval and encoding variability theories.
MAGNETOROTATIONAL-INSTABILITY-DRIVEN ACCRETION IN PROTOPLANETARY DISKS
Authors: Bai Xue-Ning
Published: September 2011

Non-ideal MHD effects play an important role in the gas dynamics in protoplanetary disks (PPDs). This paper addresses the influence of non-ideal MHD effects on the magnetorotational instability (MRI) and angular momentum transport in PPDs using the most up-to-date results from numerical simulations. We perform chemistry calculations using a complex reaction network with standard prescriptions for X-ray and cosmic-ray ionizations. We first show that whether or not grains are included, the recombination time is at least one order of magnitude less than the orbital time within five disk scale heights, justifying the validity of local ionization equilibrium and strong coupling limit in PPDs. The full conductivity tensor at different disk radii and heights is evaluated, with the MRI active region determined by requiring that (1) the Ohmic Elsasser number Λ be greater than 1 and (2) the ratio of gas to magnetic pressure β be greater than βmin(Am) as identified in the recent study by Bai & Stone, where Am is the Elsasser number for ambipolar diffusion. With full flexibility as to the magnetic field strength, we provide a general framework for estimating the MRI-driven accretion rate

and the magnetic field strength in the MRI active layer. We find that the MRI active layer always exists at any disk radius as long as the magnetic field in PPDs is sufficiently weak. However, the optimistically predicted

in the inner disk (r = 1–10 AU) appears insufficient to account for the observed range of accretion rates in PPDs (around 10−8 
M
☉ yr−1) even in the grain-free calculation, and the presence of solar abundance sub-micron grains further reduces

by one to two orders of magnitude. Moreover, we find that the predicted

increases with radius in the inner disk where accretion is layered, which would lead to runaway mass accumulation if disk accretion is solely driven by the MRI. Our results suggest that stronger sources of ionization and/or additional mechanisms such as magnetized wind are needed to explain the observed accretion rates in PPDs. In contrast, our predicted

is on the order of 10−9 
M
☉ yr−1 in the outer disk, consistent with the observed accretion rates in transitional disks.
Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation
Authors: Wu Xi , Tu Benjamin P.
Published: September 2011

Autophagy is an evolutionarily conserved pathway for the degradation of intracellular contents. How autophagy is regulated, especially upon changes in metabolic and nutritional state, remains poorly understood. By using a prototrophic strain of Saccharomyces cerevisiae, we observed that, unexpectedly, autophagy is strongly induced simply upon switch from a rich medium to a minimal medium in the complete absence of nitrogen starvation. This novel form of autophagy was termed “non-nitrogen-starvation (NNS)–induced autophagy.” A visual screen uncovered three regulators of autophagy—Iml1p, Npr2p, and Npr3p—which function in the same complex and are selectively required for NNS-induced autophagy. During NNS-induced autophagy, Iml1p localized to either preautophagosomal structures (PAS) or non-PAS punctate structures. This localization suggests that Iml1p or the Iml1p-Npr2p-Npr3p complex might regulate autophagosome formation. Ultrastructural analysis confirmed that autophagosome formation was strongly impaired in Δiml1, Δnpr2, and Δnpr3 cells during NNS-induced autophagy. Moreover, Iml1p contains a conserved domain that is required for NNS-induced autophagy as well as complex formation. Collectively, our findings have revealed the existence of additional mechanisms that regulate autophagy under previously unrecognized conditions, in response to relatively more subtle changes in metabolic and nutritional state.
The Economics of a Blender's Tax Credit versus a Tax Exemption: The Case of U.S. “Splash and Dash” Biodiesel Exports to the European Union
Authors: de Gorter Harry , Drabik Dusan , Just David R.
Published: September 2011

A conceptual framework is advanced that determines world biodiesel prices, the policy parameters in the country establishing the price, and the binding mandate or tax exemption. The effect of a tax credit differs with international trade compared to traditional closed economy analysis. The U.S. “splash & dash” program, with its $1/gallon tax credit, had minimal impacts on European Union (EU) biodiesel producer profits. Reduced world oil prices and EU tax exemptions, as well as increased rapeseed oil prices, are shown to have reduced the profitability of EU biodiesel production. EU imports from the United States can be beneficial for EU taxpayers, fuel consumers, and U.S. biodiesel producers.
wapRNA: a web-based application for the processing of RNA sequences
Authors: Zhao Wenming , Liu Wanfei , Tian Dongmei , Tang Bixia , Wang Yanqing , Yu Caixia , Li Rujiao , Ling Yunchao , Wu Jiayan , Song Shuhui , Hu Songnian
Published: September 2011

Summary: mRNA/miRNA-seq technology is becoming the leading technology to globally profile gene expression and elucidate the transcriptional regulation mechanisms in living cells. Although there are many tools available for analyzing RNA-seq data, few of them are available as easy accessible online web tools for processing both mRNA and miRNA data for the RNA-seq based user community. As such, we have developed a comprehensive web application tool for processing mRNA-seq and miRNA-seq data. Our web tool wapRNA includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data. We accept raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction. wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of gene's or miRNA's different expression in different samples. Moreover, we provide the executable packages for installation on user's local server.

Availability: wapRNA is freely available for use at http://waprna.big.ac.cn. The executable packages and the instruction for installation can be downloaded from our web site.

Contact:  husn@big.ac.cn; songshh@big.ac.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Robust relative compression of genomes with random access
Authors: Deorowicz Sebastian , Grabowski Szymon
Published: September 2011

Motivation: Storing, transferring and maintaining genomic databases becomes a major challenge because of the rapid technology progress in DNA sequencing and correspondingly growing pace at which the sequencing data are being produced. Efficient compression, with support for extraction of arbitrary snippets of any sequence, is the key to maintaining those huge amounts of data.

Results: We present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over an order of magnitude greater. In particular, 69 differentially encoded human genomes are compressed over 400 times at fast compression, or even 1000 times at slower compression (the reference genome itself needs much more space). Adding fast random access to text snippets decreases the ratio to ~300.

Availability: GDC is available at http://sun.aei.polsl.pl/gdc.

Contact:  sebastian.deorowicz@polsl.pl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Authors: Wu Jie , Akerman Martin , Sun Shuying , McCombie W. Richard , Krainer Adrian R. , Zhang Michael Q.
Published: September 2011

Motivation: Alternative splicing (AS) is a pre-mRNA maturation process leading to the expression of multiple mRNA variants from the same primary transcript. More than 90% of human genes are expressed via AS. Therefore, quantifying the inclusion level of every exon is crucial for generating accurate transcriptomic maps and studying the regulation of AS.

Results: Here we introduce SpliceTrap, a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without requiring a background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation and real data analysis, and compared it to state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness and reliability in quantifying exon-inclusion ratios.

Conclusions: SpliceTrap is a useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion ratios from RNA-seq data.

Availability and Implementation: SpliceTrap can be implemented online through the CSH Galaxy server http://cancan.cshl.edu/splicetrap and is also available for download and installation at http://rulai.cshl.edu/splicetrap/.

Contact:  michael.zhang@utdallas.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Clinical characteristics and major comorbidities in heart failure patients more than 85 years of age compared with younger age groups
Authors: Mogensen Ulrik Madvig , Ersbøll Mads , Andersen Mads , Andersson Charlotte , Hassager Christian , Torp‐Pedersen Christian , Gustafsson Finn , Køber Lars
Published: September 2011

Aims

Heart failure (HF) is increasingly prevalent among the growing number of elderly people, but not well studied. We sought to evaluate disease pattern and importance of prognostic factors among very elderly patients with HF.

Methods and results

Among 8507 patients screened for entry into two studies on HF, we analysed the clinical characteristics, major comorbidities and prognostic factors in 825 patients older than 85 years (very elderly) compared with younger age groups. Adjusted hazard ratios [HR (95% confidence intervals)] of long‐term mortality were calculated using Cox models. The very elderly were more often female (60 vs. 26%) and had a higher prevalence of preserved ejection fraction (53 vs. 36%) compared with patients younger than 65 years (P< 0.001). The prevalence of cardiovascular comorbidities increased with advancing age only until the seventh decade and then declined, resulting in the lowest prevalence of diabetes (12 vs. 16%, P< 0.001), hypertension (20 vs. 26%, P< 0.001), ischaemic heart disease (42 vs. 53%, P< 0.001), and peripheral artery disease (4 vs. 6%, P= 0.017) among the very elderly compared with patients aged <85 years. Non‐cardiovascular comorbidities generally increased linearly with age. Long‐term mortality was associated with atrial fibrillation [HR = 1.30 (1.06–1.60), P= 0.013] with greater prognostic importance in the very elderly, while ejection fraction, diabetes [HR = 1.31 (1.01–1.61), P= 0.04], and renal insufficiency [HR = 1.36 (1.13–0.63), P< 0.0001] had less prognostic importance than in younger patients (P for interactions <0.003).

Conclusion

The prevalence of cardiovascular comorbidities is lower in very elderly HF patients and has different prognostic importance.
Clinical trials update from the European Society of Cardiology Heart Failure meeting 2011: TEHAF, WHICH, CARVIVA, and atrial fibrillation in GISSI‐HF and EMPHASIS‐HF
Authors: Cleland John G.F. , Coletta Alison P. , Castiello Teresa , Clark Andrew L.
Published: September 2011

This article provides information and a commentary on key trials relevant to the pathophysiology, prevention, and treatment of heart failure (HF) presented at the European Society of Cardiology Heart Failure meeting held in Gothenburg, Sweden in May 2011. Unpublished reports should be considered as preliminary, since analyses may change in the final publication. In the TEHAF study, use of the Health Buddy® monitoring system failed to reduce the number of HF admissions compared with usual care but a subgroup of patients with more recently diagnosed HF may have benefited. In the WHICH study, some reductions in the rate of hospital stay were observed in patients who underwent a nurse‐led home‐based intervention programme following a hospital admission for an acute HF exacerbation, compared with patients who were followed in a specialized outpatient clinic. Results from CARVIVA‐HF suggest that ivabradine alone or in combination with carvedilol is safe and effective for improving exercise capacity and quality of life in HF patients on optimized angiotensin‐converting enzyme inhibitor therapy. In the GISSI‐HF study there was no difference in atrial fibrillation (AF) occurrence between the n‐3 polyunsaturated fatty acids and placebo groups. In EMPHASIS‐HF the incidence of new onset AF or flutter was reduced in patients with mild HF randomized to eplerenone compared with placebo.
A Novel Multidomain Polyketide Synthase Is Essential for Zeamine Production and the Virulence of Dickeya zeae
Authors: Zhou Jianuan , Zhang Haibao , Wu Jien , Liu Qiongguang , Xi Pinggen , Lee Jasmine , Liao Jinling , Jiang Zide , Zhang Lian-Hui
Published: September 2011

Dickeya zeae is the causal agent of the rice foot rot disease, but its mechanism of infection remains largely unknown. In this study, we identified and characterized a novel gene designated as zmsA. The gene encodes a large protein of 2,346 amino acids in length, which consists of multidomains arranged in the order of N-terminus, β-ketoacyl synthase, acyl transferase, acyl carrier protein, β-ketoacyl reductase, dehydratase. This multidomain structure and sequence alignment analysis suggest that ZmsA is a member of the polyketide synthase family. Mutation of zmsA abolished antimicrobial activity and attenuated the virulence of D. zeae. To determine the relationship between antimicrobial activity and virulence, active compounds were purified from D. zeae EC1 and were structurally characterized. This led to identification of two polyamino compounds, i.e., zeamine and zeamine II, that were phytotoxins and potent antibiotics. These results have established the essential role of ZmsA in zeamine biosynthesis and presented a new insight on the molecular mechanisms of D. zeae pathogenicity.
Arbuscular Mycorrhizal Symbiosis Limits Foliar Transcriptional Responses to Viral Infection and Favors Long-Term Virus Accumulation
Authors: Miozzi Laura , Catoni Marco , Fiorilli Valentina , Mullineaux Philip M. , Accotto Gian Paolo , Lanfranco Luisa
Published: September 2011

Tomato (Solanum lycopersicum) can establish symbiotic interactions with arbuscular mycorrhizal (AM) fungi, and can be infected by several pathogenic viruses. Here, we investigated the impact of mycorrhization by the fungus Glomus mosseae on the Tomato spotted wilt virus (TSWV) infection of tomato plants by transcriptomic and hormones level analyses. In TSWV-infected mycorrhizal plants, the AM fungus root colonization limited virus-induced changes in gene expression in the aerial parts. The virus-responsive upregulated genes, no longer induced in infected mycorrhizal plants, were mainly involved in defense responses and hormone signaling, while the virus-responsive downregulated genes, no longer repressed in mycorrhizal plants, were involved in primary metabolism. The presence of the AM fungus limits, in a salicylic acid-independent manner, the accumulation of abscissic acid observed in response to viral infection. At the time of the molecular analysis, no differences in virus concentration or symptom severity were detected between mycorrhizal and nonmycorrhizal plants. However, in a longer period, increase in virus titer and delay in the appearance of recovery were observed in mycorrhizal plants, thus indicating that the plant's reaction to TSWV infection is attenuated by mycorrhization.
High-Throughput Screening and Analysis of Genes of Xanthomonas citri subsp. citri Involved in Citrus Canker Symptom Development
Authors: Yan Qing , Wang Nian
Published: September 2011

Citrus canker is caused by Xanthomonas citri subsp. citri and is one of the most devastating diseases on citrus plants. To investigate the virulence mechanism of this pathogen, a mutant library of strain 306 containing approximately 22,000 mutants was screened for virulence-deficient mutants in grapefruit (Citrus paradise). Eighty-two genes were identified that contribute to citrus canker symptom development caused by X. citri subsp. citri. Among the 82 identified genes, 23 genes were classified as essential genes, as mutation of these genes caused severe reduction of bacterial growth in M9 medium. The remaining 59 genes were classified as putative virulence-related genes that include 32 previously reported virulence-related genes and 27 novel genes. The 32 known virulence-related genes include genes that are involved in the type III secretion system (T3SS) and T3SS effectors, the quorum-sensing system, extracellular polysaccharide and lipopolysaccharide synthesis, and general metabolic pathways. The contribution to pathogenesis by nine genes (pthA4, trpG, trpC, purD, hrpM, peh-1, XAC1230, XAC1548, and XAC3049) was confirmed by complementation assays. We further validated the mutated genes and their phenotypes by analyzing the EZ-Tn5 insertion copy number using Southern blot analysis. In conclusion, we have significantly advanced our understanding of the putative genetic determinants of the virulence mechanism of X. citri subsp. citri by identifying 59 putative virulence-related genes, including 27 novel genes.
First Report of Group 16SrXII Phytoplasma Associated with Papaya Yellows in Taiwan
Authors: Bau H. J. , Hung S. C. , Chang W. C. , Chen Y. K.
Published: September 2011

Phytoplasmas have been reported to cause various disorders in papaya (Carica papaya L.), including dieback, mosaic, and yellow crinkle in Australia, Nivun Haamir dieback in Israel, and bunchy top-like disease in Cuba (1). Papaya is an economically important crop in Taiwan, and therefore, is monitored for viral infections. In 2005, papaya plants showing chlorosis, yellows and shriveling of leaves, dieback and lateral growth of branches, bending of apical branches, latexosis of fruits, and brown necrosis in phloem tissues were observed in southern Taiwan. Examination by an electron microscope revealed the presence of pleomorphic phytoplasma cells in sieve tubes of the phloem of petioles and leaf veins of diseased plants. Total DNA was extracted individually from at least three diseased plants at each location with a commercial DNA preparation kit (Axygen Scientific, Union City, CA) and used for amplification of the phytoplasma 16S rRNA gene in PCR with universal primer pairs P1 and Tint (3). The full-length 16S rRNA gene has been amplified and cloned. Sequence analysis revealed that the fragment was 1,581 bp long (GenBank Accession No. AJ919994) and shared 99.6% sequence identity with that of the ‘Candidatus Phytoplasma solani’ reference strain (GenBank Accession No. AF248959). A virtual restriction fragment length polymorphism analysis of the 16S rDNA sequence amplified from the R16F2n/R16R2 primers (2) was performed with iPhyClassifier (4) and pDRAW32. In silico restriction analysis identified the studied papaya phytoplasma as a subgroup 16SrXII-A strain. The sequence had 97 to 98% sequence identity with papaya phytoplasmas of the 16SrXII group in Australia (GenBank Accession No. Y10095), Israel (GenBank Accession No. AY903951), and Cuba (GenBank Accession No. AY725234). The disease incidence was 30 to 35% during the 2006 to 2010 growing seasons, and field surveys indicated that the disease has spread to central Taiwan with sporadic occurrence in recent years. To our knowledge, this is the first report of phytoplasma associated with papaya yellows in Taiwan.

References: (1) Y. Arocha et al. Int. J. Syst. Evol. Microbiol. 55:2451, 2005. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Effect of ‘Candidatus Liberibacter solanacearum’ on Fitness of Its Insect Vector, Bactericera cockerelli (Hemiptera: Triozidae), on Tomato
Authors: Nachappa Punya , Shapiro Ana Austin , Tamborindeguy Cecilia
Published: September 2011

The potato/tomato psyllid, Bactericera cockerelli transmits the bacterium ‘Candidatus Liberibacter solanacearum’, also known as ‘Ca. L. psyllaurous’, which causes zebra chip disease in solanaceous crops. There have been no studies addressing the effect of the bacterial plant pathogen on the biology of its insect vector. We examined several life-history traits, including 7-day fecundity, hatching percentage, incubation time, nymphal survival percentage, nymphal development time, total development time, and sex-ratio of ‘Ca. L. solanacearum’-positive and -negative psyllid isofemale lines on tomato, as well as adult mortality index of ‘Ca. L. solanacearum’-positive and -negative insects. The only two life-history traits that differed between the ‘Ca. L. solanacearum’-positive and –negative psyllid isofemale lines were 7-day fecundity and nymphal survival percentage, which were significantly lower in ‘Ca. L. solanacearum’- positive lines. The symbiotic bacteria associated with both psyllid isofemale lines were similar, with the exception of ‘Ca. L. solanacearum’, which showed 100% infection in the ‘Ca. L. solanacearum’-positive lines and was not detected in the negative psyllid lines. These results suggest that ‘Ca. L. solanacearum' has a negative effect on population growth rate of its insect vector on tomato.
Characterization of BiofumigatedRalstonia solanacearumCells Using Micro-Raman Spectroscopy and Electron Microscopy
Authors: Paret Mathews L. , Sharma Shiv K. , Alvarez Anne M.
Published: September 2011

Essential oils of palmarosa, lemongrass, and eucalyptus have shown promise as biofumigants for control of the bacterial wilt disease of edible ginger (Zingiber officinale) caused by Ralstonia solanacearum race 4 in previous potting medium studies. Biochemical changes in R. solanacearum cells were evaluated with micro-Raman spectroscopy following treatment with essential oils at different concentrations (0.04, 0.07, and 0.14% [vol/vol] of culture medium) and changes in cell structure were observed using electron microscopy. All treatments except palmarosa oil at 0.04% caused significant reductions in levels of amino acids, purine and pyrimidine bases of nucleic acids, carbohydrates, and lipids, as indicated by significant reduction in Raman peak heights at 621, 1,003, and 1,031 inverse centimeters (cm–1) (phenylalanine); 643, 827, 852, 1,158, and 1,172 cm–1(tyrosine); 758 cm–1(tryptophan); 725, 782, 1,337, and 1,578 cm–1(adenine, cytosine plus uracil, adenine, and adenine plus guanine, respectively); 1,097 cm–1(carbohydrates); and 1,127, 1,450, and 2,932 cm–1(lipids) compared with untreated controls. Lemongrass oil treatments were the most effective in degrading cellular components. Scanning electron microscopy of palmarosa and lemongrass-oil-treated cells showed rupture of cell walls and cell debris but no degradation was noted for eucalyptus-oil-treated cells. Palmarosa- and lemongrass-oil-treated cells were positively stained with uranyl acetate when viewed by transmission electron microscopy whereas controls and eucalyptus-oil-treated cells were negatively stained, indicating that the cell membranes were intact. The viability of eucalyptus-oil-treated cells was confirmed by cell culture following treatment. Micro-Raman spectroscopy is a powerful tool which can be further employed to better understand effects of fumigants and other bactericides on bacterial cells.
Mid-Cretaceous charred fossil flowers reveal direct observation of arthropod feeding strategies
Authors: Hartkopf-Fröder Christoph , Rust Jes , Wappler Torsten , Friis Else Marie , Viehofen Agnes
Published: September 2011

Although plant–arthropod relationships underpin the dramatic rise in diversity and ecological dominance of flowering plants and their associated arthropods, direct observations of such interactions in the fossil record are rare, as these ephemeral moments are difficult to preserve. Three-dimensionally preserved charred remains of
Chloranthistemon
flowers from the Late Albian to Early Cenomanian of Germany preserve scales of mosquitoes and an oribatid mite with mouthparts inserted into the pollen sac. Mosquitoes, which today are frequent nectar feeders, and the mite were feeding on pollen at the time wildfire consumed the flowers. These findings document directly arthropod feeding strategies and their role in decomposition.
Dolphin whistles: a functional misnomer revealed by heliox breathing
Authors: Madsen P. T. , Jensen F. H. , Carder D. , Ridgway S.
Published: September 2011

Delphinids produce tonal whistles shaped by vocal learning for acoustic communication. Unlike terrestrial mammals, delphinid sound production is driven by pressurized air within a complex nasal system. It is unclear how fundamental whistle contours can be maintained across a large range of hydrostatic pressures and air sac volumes. Two opposing hypotheses propose that tonal sounds arise either from tissue vibrations or through actual whistle production from vortices stabilized by resonating nasal air volumes. Here, we use a trained bottlenose dolphin whistling in air and in heliox to test these hypotheses. The fundamental frequency contours of stereotyped whistles were unaffected by the higher sound speed in heliox. Therefore, the term whistle is a functional misnomer as dolphins actually do not whistle, but form the fundamental frequency contour of their tonal calls by pneumatically induced tissue vibrations analogous to the operation of vocal folds in terrestrial mammals and the syrinx in birds. This form of tonal sound production by nasal tissue vibrations has probably evolved in delphinids to enable impedance matching to the water, and to maintain tonal signature contours across changes in hydrostatic pressures, air density and relative nasal air volumes during dives.
Identifying mental states from neural states under mental constraints
Authors: Atmanspacher Harald
Published: September 2011

This article emphasizes how the recently proposed interlevel relation of contextual emergence for scientific descriptions combines ‘bottom-up’ and ‘top-down’ kinds of influence. As emergent behaviour arises from features pertaining to lower level descriptions, there is a clear bottom-up component. But, in general, this is not sufficient to formulate interlevel relations stringently. Higher level contextual constraints are needed to equip the lower level description with those details appropriate for the desired higher level description to emerge. These contextual constraints yield some kind of ‘downward confinement’, a term that avoids the sometimes misleading notion of ‘downward causation’. This will be illustrated for the example of relations between (lower level) neural states and (higher level) mental states.
Gait recognition: highly unique dynamic plantar pressure patterns among 104 individuals
Authors: Pataky Todd C. , Mu Tingting , Bosch Kerstin , Rosenbaum Dieter , Goulermas John Y.
Published: September 2011

Everyone's walking style is unique, and it has been shown that both humans and computers are very good at recognizing known gait patterns. It is therefore unsurprising that dynamic foot pressure patterns, which indirectly reflect the accelerations of all body parts, are also unique, and that previous studies have achieved moderate-to-high classification rates (CRs) using foot pressure variables. However, these studies are limited by small sample sizes (
n
< 30), moderate CRs (CR ≃ 90%), or both. Here we show, using relatively simple image processing and feature extraction, that dynamic foot pressures can be used to identify
n
= 104 subjects with a CR of 99.6 per cent. Our key innovation was improved and automated spatial alignment which, by itself, improved CR to over 98 per cent, a finding that pointedly emphasizes inter-subject pressure pattern uniqueness. We also found that automated dimensionality reduction invariably improved CRs. As dynamic pressure data are immediately usable, with little or no pre-processing required, and as they may be collected discreetly during uninterrupted gait using in-floor systems, foot pressure-based identification appears to have wide potential for both the security and health industries.
Dynamics of alternative modes of RNA replication for positive-sense RNA viruses
Authors: Sardanyés Josep , Martínez Fernando , Daròs José-Antonio , Elena Santiago F.
Published: September 2011

We propose and study nonlinear mathematical models describing the intracellular time dynamics of viral RNA accumulation for positive-sense single-stranded RNA viruses. Our models consider different replication modes ranging between two extremes represented by the geometric replication (GR) and the linear stamping machine replication (SMR). We first analyse a model that quantitatively reproduced experimental data for the accumulation dynamics of both polarities of turnip mosaic potyvirus RNAs. We identify a non-degenerate transcritical bifurcation governing the extinction of both strands depending on three key parameters: the mode of replication (
α
), the replication rate (
r
) and the degradation rate (
δ
) of viral strands. Our results indicate that the bifurcation associated with
α
generically takes place when the replication mode is closer to the SMR, thus suggesting that GR may provide viral strands with an increased robustness against degradation. This transcritical bifurcation, which is responsible for the switching from an active to an absorbing regime, suggests a smooth (i.e. second-order), absorbing-state phase transition. Finally, we also analyse a simplified model that only incorporates asymmetry in replication tied to differential replication modes.
Nonlinear stability criteria for tree-like structures composed of branched elastic rods
Authors: O'Reilly Oliver M. , Peters Daniel M.
Published: September 2011

New necessary conditions for the nonlinear stability of branched tree-like structures composed of elastic rods are presented. The conditions, which are found by examining the second variation of an energy functional, are established by extending Legendre's classical work on this topic. For the branched tree-like structures of interest in this paper, one of the new necessary conditions is the existence of a bounded solution to a set of Riccati equations, which are coupled at branching points. In addition, a set of new necessary conditions are established in the event that the abscissa of the branching point is not fixed. The results are illustrated using a range of examples featuring planar configurations of branched elastic rods where each of the individual rods is modelled using Euler's theory of the elastica.
Extended time-dependent mild-slope and wave-action equations for wave–bottom and wave–current interactions
Authors: Toledo Yaron , Hsu Tai-Wen , Roland Aron
Published: September 2011

Extended mild-slope (MS) and wave-action equations (WAEs) are derived by taking into account high-order derivatives of the bottom profile and the depth-averaged current that were previously neglected. As a first step for this derivation, a time-dependent MS-type equation in the presence of ambient currents that consists of these high-order components is constructed. This mild-slope equation is used as a basis to form a wave-action balance equation that retains high-order refraction and diffraction terms of varying depths and currents. The derivation accurately accounts for the effects of the currents on the Doppler shift. This results in an ‘effective’ intrinsic frequency and wavenumber that differ from the ones of wave ray theory. Finally, the new WAE is derived for the phase-averaged frequency-direction spectrum in order to allow its use in stochastic wave-forecasting models.
Multiple cenozoic invasions of Africa by penguins (Aves, Sphenisciformes)
Authors: Ksepka Daniel T. , Thomas Daniel B.
Published: September 2011

Africa hosts a single breeding species of penguin today, yet the fossil record indicates that a diverse array of now-extinct taxa once inhabited southern African coastlines. Here, we show that the African penguin fauna had a complex history involving multiple dispersals and extinctions. Phylogenetic analyses and biogeographic reconstructions incorporating new fossil material indicate that, contrary to previous hypotheses, the four Early Pliocene African penguin species do not represent an endemic radiation or direct ancestors of the living
Spheniscus demersus
(blackfooted penguin). A minimum of three dispersals to Africa, probably assisted by the eastward-flowing Antarctic Circumpolar and South Atlantic currents, occurred during the Late Cenozoic. As regional sea-level fall eliminated islands and reduced offshore breeding areas during the Pliocene, all but one penguin lineage ended in extinction, resulting in today's depleted fauna.
Separable temporal metrics for time perception and anticipatory actions
Authors: Marinovic Welber , Arnold Derek H.
Published: September 2011

Reliable estimates of time are essential for initiating interceptive actions at the right moment. However, our sense of time is surprisingly fallible. For instance, time perception can be distorted by prolonged exposure (adaptation) to movement. Here, we make use of this to determine if time perception and anticipatory actions rely on the same or on different temporal metrics. Consistent with previous reports, we find that the apparent duration of movement is mitigated by adaptation to more rapid motion, but is unchanged by adaptation to slower movement. By contrast, we find symmetrical effects of motion-adaptation on the timing of anticipatory interceptive actions, which are paralleled by changes in perceived speed for the adapted direction of motion. Our data thus reveal that anticipatory actions and perceived duration rely on different temporal metrics.
Chromosomes Carrying Meiotic Avoidance Loci in Three Apomictic Eudicot Hieracium Subgenus Pilosella Species Share Structural Features with Two Monocot Apomicts
Authors: Okada Takashi , Ito Kanae , Johnson Susan D. , Oelkers Karsten , Suzuki Go , Houben Andreas , Mukai Yasuhiko , Koltunow Anna M.
Published: September 2011

The LOSS OF APOMEIOSIS (LOA) locus is one of two dominant loci known to control apomixis in the eudicot Hieracium  praealtum. LOA stimulates the differentiation of somatic aposporous initial cells after the initiation of meiosis in ovules. Aposporous initial cells undergo nuclear proliferation close to sexual megaspores, forming unreduced aposporous embryo sacs, and the sexual program ceases. LOA-linked genetic markers were used to isolate 1.2 Mb of LOA-associated DNAs from H. praealtum. Physical mapping defined the genomic region essential for LOA function between two markers, flanking 400 kb of identified sequence and central unknown sequences. Cytogenetic and sequence analyses revealed that the LOA locus is located on a single chromosome near the tip of the long arm and surrounded by extensive, abundant complex repeat and transposon sequences. Chromosomal features and LOA-linked markers are conserved in aposporous Hieracium  caespitosum and Hieracium  piloselloides but absent in sexual Hieracium  pilosella. Their absence in apomictic Hieracium  aurantiacum suggests that meiotic avoidance may have evolved independently in aposporous subgenus Pilosella species. The structure of the hemizygous chromosomal region containing the LOA locus in the three Hieracium subgenus Pilosella species resembles that of the hemizygous apospory-specific genomic regions in monocot Pennisetum squamulatum and Cenchrus ciliaris. Analyses of partial DNA sequences at these loci show no obvious conservation, indicating that they are unlikely to share a common ancestral origin. This suggests convergent evolution of repeat-rich hemizygous chromosomal regions containing apospory loci in these monocot and eudicot species, which may be required for the function and maintenance of the trait.
A Wheat Homolog of MOTHER OF FT AND TFL1 Acts in the Regulation of Germination
Authors: Nakamura Shingo , Abe Fumitaka , Kawahigashi Hiroyuki , Nakazono Kou , Tagiri Akemi , Matsumoto Takashi , Utsugi Shigeko , Ogawa Taiichi , Handa Hirokazu , Ishida Hiroki , Mori Masahiko , Kawaura Kanako , Ogihara Yasunari , Miura Hideho
Published: September 2011

Seed dormancy is an adaptive mechanism and an important agronomic trait. Temperature during seed development strongly affects seed dormancy in wheat (Triticum aestivum) with lower temperatures producing higher levels of seed dormancy. To identify genes important for seed dormancy, we used a wheat microarray to analyze gene expression in embryos from mature seeds grown at lower and higher temperatures. We found that a wheat homolog of MOTHER OF FT AND TFL1 (MFT) was upregulated after physiological maturity in dormant seeds grown at the lower temperature. In situ hybridization analysis indicated that MFT was exclusively expressed in the scutellum and coleorhiza. Mapping analysis showed that MFT on chromosome 3A (MFT-3A) colocalized with the seed dormancy quantitative trait locus (QTL) QPhs.ocs-3A.1. MFT-3A expression levels in a dormant cultivar used for the detection of the QTL were higher after physiological maturity; this increased expression correlated with a single nucleotide polymorphism in the promoter region. In a complementation analysis, high levels of MFT expression were correlated with a low germination index in T1 seeds. Furthermore, precocious germination of isolated immature embryos was suppressed by transient introduction of MFT driven by the maize (Zea mays) ubiquitin promoter. Taken together, these results suggest that MFT plays an important role in the regulation of germination in wheat.
Characterization of the time-dependentL-asparagine monohydrate crystal phase transition
Authors: de Menezes A. S. , Ardito F. M. , dos Santos A. O. , Moreno A. J. D. , Lima R. J. C. , Hayashi M. A. , Cardoso L. P.
Published: September 2011

The high-temperature phase transition of single crystals of L-asparagine monohydrate was investigated by X-ray diffraction in association with Rietveld refinement and dilatometer measurements as a function of annealing time. The X-ray results showed that, for samples annealed at 343 K (or even 333 K) for 5 h, the expected anhydrous L-asparagine phase has been formed, monoclinic system (space groupP21), with lattice parametersa= 5.0677 (2),b= 6.7657 (2),c = 8.0742 (3) Å and β = 91.276 (4)°. The results obtained from measurements as a function of annealing time confirmed that the phase transition associated with loss of the water molecule is time dependent.
Skin delivery of short hairpin RNA of indoleamine 2,3 dioxygenase induces antitumor immunity against orthotopic and metastatic liver cancer
Authors: Huang Tzu‐Ting , Yen Meng‐Chi , Lin Chi‐Chen , Weng Tzu‐Yang , Chen Yi‐Ling , Lin Chiu‐Mei , Lai Ming‐Derg
Published: September 2011

Liver cancer is one of the most malignant cancers in the world and has a high rate of metastasis. Therefore, development of a novel therapy for liver cancer is a critical issue. Indoleamine 2,3‐dioxygenase (IDO) is known as a negative immune regulator in dendritic cells. Our previous study demonstrated that skin delivery of IDO short hairpin RNA (shRNA) induced antitumor immunity in subcutaneous bladder and colon tumor models. Because the immunological environment is quite different between skin and liver, it is essential to evaluate whether skin delivery of IDO shRNA is an effective treatment in metastatic and orthotopic animal tumor models. In the present study, IDO shRNA inhibited tumor growth in subcutaneous, metastatic and orthotopic liver tumor models. The cytotoxicity of splenocytes was significantly elevated in mice treated with IDO shRNA in the orthotopic and metastatic tumor models. Interleukin (IL)‐12 and interferon (IFN)‐gamma mRNA expression were upregulated while IL‐10 was downregulated in the inguinal lymph nodes, which were collected from IDO shRNA‐treated mice. Similar results were observed in the spleens of mice inoculated with IDO shRNA by gene gun. The results indicate that skin administration of IDO shRNA is an effective therapy in orthotopic and metastatic liver cancer animal models. Indoleamine 2,3‐dioxygenase shRNA might be a potential new treatment for liver cancer in the future. (Cancer Sci 2011; 102: 2214–2220)
Reduction of nitric oxide level enhances the radiosensitivity of hypoxic non‐small cell lung cancer
Authors: Saleem Wael , Suzuki Yoshiyuki , Mobaraki Abdulelah , Yoshida Yukari , Noda Shinei , Saitoh Jun‐ich , Nakano Takashi
Published: September 2011

The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (E‐TKI) resistance has emerged as an important clinical issue. To overcome this resistance, researchers have examined different modalities, either for use as a monotherapy or in combination with E‐TKI therapy. In the present study, we investigated whether a decrease in nitric oxide (NO) levels affects the radiosensitization of non‐small cell lung cancer (NSCLC) cell lines. A549 and H3255 NSCLC cells were examined. They were subjected to hypoxic conditions and monotherapy, or combined therapy using radiation and NG‐monomethyl‐l‐arginine, monoacetate (LNMMA). Reductions in nitric oxide levels enhanced the radiosensitivity of both cell lines and significantly reduced the expression of both hypoxia‐inducible factor‐1α (HIF‐1α) and EGFR in H3255 cells compared to A549 cells. Since NO is significantly associated with cell metabolism, we measured the levels of pyruvate dehydrogenase kinase‐1 (PDK‐1), reactive oxygen species, and oxygen and observed that the expression of PDK‐1 was significantly reduced. This reduction was seen simultaneously after the silencing of HIF‐1α; however, not following LNMMA treatment. The oxygen concentration was significantly increased in the treated cells, and their viability decreased in parallel. Reactive oxygen species were decreased after LNMMA and radiation treatment. Adding EGFR–TKI to cells with reduced NO levels further suppressed cell viability when combined with radiation. This study suggests that a reduction in the NO level might substantially overcome the radioresistance of mutant NSCLC cells. (Cancer Sci 2011; 102: 2150–2156)
Brief exposures of human body lice to sublethal amounts of ivermectin over‐transcribes detoxification genes involved in tolerance
Authors: Yoon K. S. , Strycharz J. P. , Baek J. H. , Sun W. , Kim J. H. , Kang J. S. , Pittendrigh B. R. , Lee S. H. , Clark J. M.
Published: September 2011

Transcriptional profiling results, using our non‐invasive induction assay {short exposure intervals (2–5 h) to sublethal amounts of insecticides [<lethal concentration 3% (LC3) at 24 h] administered by stress‐reducing means (contact vs. immersion screen) and with induction assessed in a time frame when tolerance is still present [∼lethal concentration 90% (LC90) in 2–4 h]}, showed that ivermectin‐induced detoxification genes from body lice are identified by quantitative real‐time PCR analyses. Of the cytochrome P450 monooxygenase and ATP binding cassette transporter genes induced by ivermectin, CYP6CJ1, CYP9AG1, CYP9AG2 and PhABCC4 were respectively most significantly over‐expressed, had high basal expression levels and were most closely related to genes from other organisms that metabolized insecticides, including ivermectin. Injection of double‐stranded RNAs (dsRNAs) against either CYP9AG2 or PhABCC4 into non‐induced female lice reduced their respective transcript level and resulted in increased sensitivity to ivermectin, indicating that these two genes are involved in the xenobiotic metabolism of ivermectin and in the production of tolerance.