bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Bacillus Calmette‐Guerin in a Mouse Model of Allergic Rhinitis
Authors: Kim Soo Whan , Yeo Sang Won
Published: May 2007

OBJECTIVE

To develop an allergic rhinitis model via local sensitization of mice with Dermatophagoides pteronyssinus and to use the model to investigate the antiallergic effect of Bacillus Calmette‐Guerin (BCG).

METHODS

BALB/c mice were randomized to the allergic rhinitis group, the BCG group sensitized with D pteronyssinus via local sensitization for 7 weeks, or the control group. The BCG group received 1 × 105 colony‐forming unit/mL of BCG seven times. We evaluated symptoms, nasal mucosa eosinophilia, serum total IgE, cytokines, and eosinophilia in bronchoalveolar lavage fluid.

RESULTS

In the allergic rhinitis group, allergy symptoms (P < 0.001), eosinophil count (P < 0.001), total IgE (P < 0.001), inflammatory cells (P < 0.01), and IL‐13 (P = 0.046) increased and interferon γ (IFN‐γ) (P < 0.001) decreased compared with the control group. In the BCG group, allergy symptoms (P < 0.001), eosinophil count (P < 0.001), and inflammatory cells (P < 0.01) decreased and IFN‐γ (P = 0.031) increased compared with the allergic rhinitis group.

CONCLUSION

In an allergic rhinitis animal model developed via local sensitization of mice with D pteronyssinus, BCG was shown to exhibit an antiallergic effect.
Malignant Parotid Tumor and Facial Palsy
Authors: Tseng Fen‐Yu , Chen Zeng‐Chang , Hsu Chuan‐Jen , Ko Jeng‐Yuh , Lou Pei‐Jen , Chen Yuh‐Shyang
Published: May 2007

OBJECTIVE

To evaluate risk factors for postoperative facial palsy in patients with parotid carcinoma.

STUDY DESIGN AND SETTING

We conducted a retrospective chart review of patients with parotid carcinoma who underwent parotidectomy at National Taiwan University Hospital from 1980 to 2000.

RESULTS

Eighty‐eight patients with a mean age of 53 ± 17 y were recruited. Sixty patients (68.2%) experienced postoperative facial palsy. Tumor size of larger than 4 cm was associated with an increased incidence of facial palsy (P = 0.0422). Facial palsy was noted in 95.5 percent of patients with facial nerve involvement and 51.3 percent of patients without facial nerve involvement (P = 0.0004). Of 42 patients with tumor over the deep lobe, 37 (88.1%) had facial palsy but only 50 percent (23 of 46) of those with tumor over the superficial lobe had facial palsy (P = 0.0001).

CONCLUSION

There were no significant associations between histopathology and facial palsy. Increasing tumor size, deep lobe tumor location, and tumor invasion of facial nerve increased the incidence of postparotidectomy facial palsy.

SIGNIFICANCE

By paying attention to these risk factors a reduction of postoperative facial nerve palsy my be achieved.
Phase‐Shift Treatment for Predominant Tone Tinnitus
Authors: Lipman Ruthann I. , Lipman Sidney P.
Published: May 2007

OBJECTIVES

To independently evaluate phase‐shift treatment for predominant tone tinnitus.

STUDY DESIGN

Prospective, single‐blinded crossover study.

METHODS

61 subjects with predominant tone tinnitus participated in 2 weeks of control and 2 weeks of phase‐shift treatment. Frequency and intensity matching, pre‐ and post‐treatment tinnitus handicap inventory (THI) scores, and patient diaries were outcome measures.

RESULTS

Initial volume comparisons show a strong relationship between treatment and decrease in tinnitus intensity, with 57% of patients achieving successful treatment. Thirty‐seven percent decreased by one THI grade, 5% by two. Utilizing patient diaries, 42% of patients reported periods of complete residual inhibition (CRI) ranging from 1 hour to 7 days (average 2 days). No periods of CRI were reported in control weeks.

CONCLUSION

Phase‐shift treatment significantly benefited the majority of our patients. These outcomes suggest that this device may be a valuable tool. Further long‐term studies with home therapy are warranted.
Pediatric Microvascular Reconstruction: A Report from the Microvascular Committee
Authors: Arnold David J. , Wax Mark K.
Published: May 2007

BACKGROUND

Free tissue transfer is an integral part of modern head and neck surgery in the adult population. Its use in the pediatric population has not been well described. Recently, there has been an increase in the application of these techniques in the pediatric population. The morbidity of free tissue transfer in small pediatric patients and its effect on growth has not been well described.

OBJECTIVE

To evaluate the utility of microvascular reconstruction techniques in the pediatric population.

STUDY DESIGN

A consensus study was performed by the microvascular committee of the American Academy of Otolaryngology‐Head and Neck Surgery. Thirty active microvascular surgeons reviewed their databases to find patients less than 21 years of age who underwent free tissue transfer.

RESULTS

49 free tissue transfers performed between 1999 and 2005. The mean age was 12.1 years (age range, 3–21). The types of flaps transferred were radial forearm (10), fibula (21), rectus abdominus (7), scapula (1), latissimus dorsi (3), groin (1), gracillus (4), and jejunum (2). Morbidity at the donor site was relatively minimal. Five patients developed wound breakdown. One of these required return to the operating room. Morbidity at the reconstructed site was also rare. Patients were followed for an average of 49 months (range, 1–131 months), and no problems were noted with growth at the donor or recipient sites.

CONCLUSIONS

Free flaps in the pediatric population have morbidity and survival similar to those in the adult population.

SIGNIFICANCE

While indications differ from those in the adult population, these techniques are viable and valuable and should be considered in the pediatric reconstructive paradigm.
Head and Neck Manifestations and Quality of Life of Patients with Ectodermal Dysplasia
Authors: Mehta Umang , Brunworth Joseph , Fete Timothy J. , Sindwani Raj
Published: May 2007

OBJECTIVES

Ectodermal dysplasias (EDs) are a group of genetic disorders characterized by deficient ectodermal and mesodermal development. Studies examining resultant otolaryngologic issues are few. The objectives of this study were to delineate the head and neck manifestations and quality of life in EDs.

STUDY DESIGN AND SETTING

For 75 individuals, comprehensive histories were taken and otolaryngologic examinations were performed, and subjects rated their otolaryngologic symptom severity. A validated quality of life instrument (SF‐8) was administered.

RESULTS

The majority of subjects had a diagnosis of hypohidrotic ED (72%). Otolaryngologic conditions included otitis media (28%), cerumen impaction (48%), nasal obstruction/crusting (51%), heat intolerance (76%), and eczema (39%). Physical findings included peg teeth/hypodontia (76%), alopecia (41%), nasal crusting (41%), and saddle nose deformity (44%). Quality of life scores were generally high. Overall, health was rated “good to excellent” by 87 percent.

CONCLUSION

Patients with ED frequently experience significant otolaryngologic symptoms, although most patients report a good quality of life.

SIGNIFICANCE

A greater understanding of the otolaryngologic issues in ED should help facilitate diagnosis and improve management.
Neue Aspekte bei Hyperparathyreoidismus
Authors: Kruse  , Beige
Published: May 2007

Das Krankheitsbild des Hyperparathyreoidismus wird in eine primäre und eine sekundäre Form unterteilt. Der primäre Hyperparathyreoidismus entsteht durch eine autonome Hypertrophie und/oder Hyperplasie einer oder mehrerer Nebenschilddrüsen, in den meisten Fällen ohne bekannte Ursache. Das erhöhte Parathormon verursacht durch Mobilisation des Kalziums aus dem Knochen eine Serumhyperkalzämie und Osteopenie, cerebrale Symptome, Müdigkeit und Verkalkungen von Nieren und Gefäßen. Der sekundäre Hyperparathyreoidismus entsteht als Regulativ bei Mangel an aktivem Vitamin D3, Hypokalzämie oder Hyperphosphatämie, zum Beispiel im Rahmen einer Niereninsuffizienz. Durch die gesteigerte Parathormonsekretion kann das Serumkalzium und initial auch das -phosphat im Normbereich gehalten werden. Die andauernde Stimulation verursacht im Verlauf eine Hyperplasie der Nebenschilddrüsen. Die Therapie des Hyperparathyreoidismus richtet sich nach dem jeweiligen zugrundeliegenden pathophysiologischen Mechanismus. Während die chirurgische Entfernung der vergrößerten Nebenschilddrüse(n) bei primären und nicht kontrollierten sekundären Formen der einzige kurative Ansatz ist, sind Vitamin D Substitution, Phosphatkontrolle und der Einsatz von Calcimimetica bei frühen Formen des sekundären Hyperparathyreoidismus die Therapie der Wahl.
Hungriger Knochen nach Parathyreoidektomie – Das «Hungry Bone Syndrome»
Authors: Farese
Published: May 2007

Das Hungry Bone Syndrome (HBS) stellt eine wichtige Differentialdiagnose einer prolongierten Hypokalzämie nach Parathyreoidektomie (PTX) dar. Das HBS tritt als Folge des plötzlichen, postoperativen «PTH Entzuges» bei einer über längere Zeit vorbestehenden Mineralisationsstörung des Knochens im Rahmen eines primären, sekundären oder tertiären Hyperparathyreoidismus auf. Als Risikofaktoren für die Entwicklung des HBS sind die Adenomgröße, das Alter des Patienten, ein stark erhöhtes Serum PTH sowie ein erhöhtes Serum Kalzium und eine Serum alkalische Phosphatase präoperativ bekannt. Die Diagnose des HBS unmittelbar nach PTX erfordert eine enge klinische und laborchemische Überwachung. Therapeutisches Ziel ist die Korrektur der Elektrolytstörung mit oralem Kalzium, aktivem Vitamin D und bei schweren Verläufen auch mit intravenöser Kalziumgabe. Je nach klinischem Verlauf ist die Substitution mit Kalzium, bei niereninsuffizienten Patienten auch die Vitamin D-Gabe, über mehrere Monate bis Jahre notwendig. Als Prophylaxe eines HBS kann bei Risikopatienten präoperativ eine vorsichtige Vitamin D-Substitution indiziert sein.
Mauna Loa's submarine western flank: Landsliding, deep volcanic spreading, and hydrothermal alteration
Authors: Morgan Julia K. , Clague David A. , Borchers Deanna C. , Davis Alicé S. , Milliken Kitty L.
Published: May 2007

Four new remotely operated vehicle dives carried out by Monterey Bay Aquarium Research Institute (MBARI) reveal a heterogeneous distribution of lithologies and compositions along a transect across the submarine west flank of Mauna Loa, from the outer scarp of the frontal bench to the upper flank. The frontal bench is composed predominantly of volcaniclastic sediments, ranging from very fine‐grained monomictic hyaloclastites to coarse‐grained, compositionally mixed volcaniclastic breccias. The predominance of subaerially derived clasts suggests accumulations of landslide deposits, probably emplaced along a regional shear plane preserved in cataclastic breccias with local foliations and grain trails. Repeated packages of inversely graded strata are interpreted to reflect thrust imbrication of the resulting volcaniclastic apron during volcanic spreading of Mauna Loa's western flank, similar to that now documented along Kīlauea's south flank. Many of the rocks from the bench show evidence for alteration, ranging from low‐grade burial diagenesis to higher‐grade hydrothermal alteration, including phases never before observed in submarine Hawaiian rocks, including epidote, talc, sphene, and corrensite. Alteration is concentrated in deformed zones, denoting pathways for fluid flow into or out of the volcanic edifice. Formed at depth, the altered rocks were subsequently transported along low‐angle thrust faults into the bench and exposed along high‐angle fractures and faults. The upper submarine flanks are draped by subaerially erupted, submarine emplaced pillow lavas and interbedded hyaloclastites, generated by shoreline‐crossing lava flows. Basalt glasses indicate Mauna Loa origin but imply earlier compositions than present‐day lavas, consistent with Ar‐Ar ages suggesting eruption 0.28 ± 0.10 Ma. Late stage detachment of a nearshore slump produced the 'Ālika 2 debris avalanche that broke through the frontal bench, perhaps portending the evolution of the active Hilina slump now present on Kīlauea volcano's south flank.
Long‐range transport of the April 2001 dust clouds over the subtropical East Asia and the North Pacific and its impacts on ground‐level air pollution: A Lagrangian simulation
Authors: Wang Kuo‐Ying
Published: May 2007

One of the most remarkable Asian dust storms occurred in April 2001, during the periods of the Aerosol Characterization Experiment (ACE)‐Asia and the Transport and Chemical Evolution Over the Pacific (TRACE‐P) field experiments. Our high‐resolution Lagrangian simulations and the detailed comparisons with the Total Ozone Mapping Spectrometer (TOMS)‐Aerosol Index (AI) data, the Geostationary Meteorological Satellite (GMS)‐5 derived dust distribution, and the ground‐level ambient air particulate matter measurements over Taiwan in the subtropical East Asia reveal several features which were not reported before. We found that (1) the trans‐Pacific long‐range transport was dominated by the dust emissions from the natural source over the Gobi desert and the anthropogenic source over east China before 6–7 April, while the southward long‐range transport to the subtropical East Asia were mainly contributed by the dust emissions from natural source over the Taklamakan and the Gobi, and the anthropogenic source over east China after 6–7 April; (2) the southward long‐range transport implies that the anthropogenic pollution is ahead of the cold front (where the precipitation washes out the particulate matter), while the dust is behind the cold front. (3) The dust emissions from the Gobi during 7–9 April, anthropogenic emissions from east China during 9–10 April, and dust emissions from the Taklamakan during 1–4 April appear to have the most significant impacts on the ground‐level particulate matter concentrations over Taiwan. The simulated particle emitted from desert regions before 6–7 April mainly confined to the Gobi and the Taklamakan regions until 6 April when they became highly mobile for the long‐range transport by the large‐scale cyclonic activity and its associated cold air outbreak. The southward transport characteristics simulated here are consistent with the aerosol characterization observed at Taiwan during this period. Our simulations reveal that the rapid trans‐Pacific transport processes occurred on 12 April contribute to the extensive areas of elevated AI values prevail over the North Pacific during this day.
An evaluation of deep soil configurations in the CLM3 for improved representation of permafrost
Authors: Alexeev V. A. , Nicolsky D. J. , Romanovsky V. E. , Lawrence D. M.
Published: May 2007

A thin layer of soil used in many coupled global climate models does not resolve the heat reservoir represented by underlying ground material. Under representation of this feature leads to unrealistic simulation of temperature dynamics in the active layer and permafrost. Using the Community Land Model (CLM3) and its modifications we estimate a required thickness of soil layers to calculate temperature dynamics within certain errors. Our results show that to compute the annual cycle of temperature dynamics for cold permafrost, the soil thickness should be at least 30 meters. Decadal‐to‐century time scales require significantly deeper soil layers, e.g. hundreds of meters. We also tested a new geometrical configuration of the soil layer geometry which is called slab permafrost. This configuration is represented by a thick soil layer underneath the traditional resolved soil layer. The model configuration with 30 m deep resolved soil layer and a 30 to 100 m thick slab shows results that favorably compare with our benchmark model which has a fully resolved 300 m‐deep soil layer.
Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment
Authors: Hewson Ian , Moisander Pia H , Morrison Amanda E , Zehr Jonathan P
Published: May 2007

We investigated diazotrophic bacterioplankton assemblage composition in the Heron Reef lagoon (Great Barrier Reef, Australia) using culture-independent techniques targeting the nifH fragment of the nitrogenase gene. Seawater was collected at 3 h intervals over a period of 72 h (i.e. over diel as well as tidal cycles). An incubation experiment was also conducted to assess the impact of phosphate (PO43−) availability on nifH expression patterns. DNA-based nifH libraries contained primarily sequences that were most similar to nifH from sediment, microbial mat and surface-associated microorganisms, with a few sequences that clustered with typical open ocean phylotypes. In contrast to genomic DNA sequences, libraries prepared from gene transcripts (mRNA amplified by reverse transcription-polymerase chain reaction) were entirely cyanobacterial and contained phylotypes similar to those observed in open ocean plankton. The abundance of Trichodesmium and two uncultured cyanobacterial phylotypes from previous studies (group A and group B) were studied by quantitative-polymerase chain reaction in the lagoon samples. These were detected as transcripts, but were not detected in genomic DNA. The gene transcript abundance of these phylotypes demonstrated variability over several diel cycles. The PO43− enrichment experiment had a clearer pattern of gene expression over diel cycles than the lagoon sampling, however PO43− additions did not result in enhanced transcript abundance relative to control incubations. The results suggest that a number of diazotrophs in bacterioplankton of the reef lagoon may originate from sediment, coral or beachrock surfaces, sloughing into plankton with the flooding tide. The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef.
New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation
Authors: Francis Christopher A , Beman J Michael , Kuypers Marcel M M
Published: May 2007

Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.
Decision‐making by the immune response
Authors: Callard Robin E
Published: May 2007

Decisions by uncommitted cells to differentiate down one lineage pathway or another is fundamental to developmental biology. In the immune system, lymphocyte precursors commit to T‐ or B‐cell lineages and T‐cell precursors to CD4 or CD8 independently of foreign antigen. T and B cells must also decide whether or not to respond to antigen and when a response is initiated, what sort of response to make such as the type of antibody, CD4 or CD8, and CD4 Th1 or Th2. The two basic mechanisms for these decision‐making processes are selection and instruction. Selection depends on prior stochastic production of precommitted cells, which are then selected to respond by an appropriate signal; for example, CD8 and CD4 responses selected by peptide presented in association with major histocompatibility complex class I or II. In contrast, instruction occurs when an uncommitted precursor embarks upon a differentiation pathway in response to a particular set of signals; for example, Th1 and Th2 lineage commitment. In this paper, the signals that determine Th1 and Th2 differentiation are examined with a mathematical model and shown to act as a bistable switch permitting either Tbet or Gata3 to be expressed in an individual cell but not both. The model is used to show how the Tbet Gata3 network within an individual cell interacts with cytokine signals between cells and suggests how Th1 and Th2 lineage commitment can become irreversible. These considerations provide an example of how mathematical models can be used to gain a better understanding of lymphocyte differentiation in an immune response.
Flow, flow shear, and related profiles in helicon plasmas
Authors: Scime E. , Hardin R. , Biloiu C. , Keesee A. M. , Sun X.
Published: May 2007

Measurements of the three-dimensional ion flow field and the ion temperature in a cross section of a cylindrical, argon, helicon plasma are presented. When these measurements are combined with radially resolved measurements of the plasma density, electron temperature, neutral density, and neutral temperature, the radial profiles of the ion viscosity and ion-neutral momentum transfer rate can be calculated. The ion viscosity and ion-neutral momentum transfer rate profiles are important input parameters for theoretical models of azimuthal flows arising from the nonlinear interaction of drift waves in helicon sources. The experimentally determined magnitudes and radial profiles reported in this work are significantly different than those used in recent theoretical studies. Measurements of the radial flow of argon neutrals and helium neutrals are also presented for a helicon plasma.
Displacements of Sb atoms in supersaturated Sb-doped Si layer formed by molecular beam epitaxy growth
Authors: Zhu Lei , Thompson Phillip E. , Zhang Xinghang , Hollander Mark , Shao Lin
Published: May 2007

Rutherford backscattering channeling measurements with angular scans have been carried out on ⟨100⟩ Sb-doped Si superlattice structures formed by molecular beam epitaxy growth. Three different crystallographic axes ⟨100⟩, ⟨111⟩, and ⟨110⟩ have been explored. We have observed Sb displacements from their substitutional sites with displacement amplitudes of 0.22 Å in as-grown samples. The displacements increase with increasing post-growth annealing temperatures, associated with formation of nanometer size Sb precipitates.
Quantitative numerical and experimental studies of the shock accelerated heterogeneous bubbles motion
Authors: Layes G. , Le Métayer O.
Published: May 2007

This work deals with quantitative comparisons between experimental and numerical results for shock-bubbles interactions. The bubbles are filled with three different gases (nitrogen, krypton and helium) surrounded by air in order to investigate all kind of density jumps across the interface. For each case, three incident shock wave intensities are also studied. The experiments are led by using a shock tube coupled with a visualization diagnostic device: the T80 shock tube [G. Jourdan, L. Houas, L. Schwaederlé, G. Layes, R. Carrey, and F. Diaz, “A new variable inclination shock tube for multiple investigations,” Shock Waves 13, 501 (2004)]. Considering the same initial and geometrical conditions, the numerical results are obtained with the help of a recent numerical method: the discrete equations method [R. Abgrall and R. Saurel, “Discrete equations for physical and numerical compressible multiphase mixtures,” J. Comput. Phys. 186, 361 (2003); R. Saurel, S. Gavrilyuk, and F. Renaud, “A multiphase model with internal degrees of freedom: Application to shock-bubble interaction,” J. Fluid Mech. 495, 283 (2003); A. Chinnayya, E. Daniel, and R. Saurel, “Modelling detonation waves in heterogeneous energetic materials,” J. Comput. Phys. 196, 490 (2004); O. Le Métayer, J. Massoni, and R. Saurel, “Modelling evaporation fronts with reactive Riemann solvers,” J. Comput. Phys. 205, 567 (2005)], devoted to the computation of interface problems as well as multiphase mixtures. For each configuration, the quantitative comparisons are in good agreement showing the capability of both methods (numerical and experimental) to describe complex physical flows.
High-efficiency blue multilayer polymer light-emitting diode based on poly(9,9-dioctylfluorene)
Authors: Tseng Shin-Rong , Li Shiuan-Yi , Meng Hsin-Fei , Yu Yi-Hsiang , Yang Chia-Ming , Liao Hua-Hsien , Horng Sheng-Fu , Hsu Chian-Shu
Published: May 2007

A highly efficient blue polymer light-emitting diode based exclusively on commercial poly(9,9-dioctylfluorene) and poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4′-(N-(4-s-butylphenyl)) diphenylamine)] is demonstrated. High electroluminescent efficiency is achieved by enhancing electron currents and making devices in multilayered structures. CsF∕Al is used as the efficient electron injection cathode, and the fabrication process is in the glove box to enhance electron mobility by reducing oxygen adsorption. The multilayer structure is prepared by the liquid buffer layer technique. The maximum efficiency is 2.5 cd∕A at deep blue with the corresponding external quantum efficiency of 2%.
Energy functions for rubber from microscopic potentials
Authors: Johal A. S. , Dunstan D. J.
Published: May 2007

The finite deformation theory of rubber and related materials is based on energy functions that describe the macroscopic response of these materials under deformation. Energy functions and elastic constants are here derived from a simple microscopic (ball-and-spring) model. Exact uniaxial force-extension relationships are given for Hooke’s Law and for the thermodynamic entropy-based microscopic model using the Gaussian and the inverse Langevin statistical approximations. Methods are given for finding the energy functions as expansions of tensor invariants of deformation, with exact solutions for functions that can be expressed as expansions in even powers of the extension. Comparison with experiment shows good agreement with the neo-Hookean energy function and we show how this derives directly from the simple Gaussian statistical model with a small modification.
Enhanced Raman scattering in thermally poled sodium-niobium borophosphate glasses
Authors: Dussauze Marc , Fargin Evelyne , Rodriguez Vincent , Malakho Artem , Kamitsos Efstratios
Published: May 2007

Micro-Raman analysis has been carried out on the cross section of thermally poled sodium-niobium borophosphate glasses. We were able to measure with accuracy an enhanced Raman response from the nonlinear optical (NLO) layer formed at the anode side of the poled glasses. The thickness of the NLO layer has been estimated. Several spectral changes were observed within this layer, which manifest important structural rearrangements after thermal poling. Possible mechanisms leading to structural reorganization in the space charge region are discussed.
Shearing instabilities accompanying high-pressure phase transformations and the mechanics of deep earthquakes
Authors: Green Harry W.
Published: April 2007

Deep earthquakes have been a paradox since their discovery in the 1920s. The combined increase of pressure and temperature with depth precludes brittle failure or frictional sliding beyond a few tens of kilometers, yet earthquakes occur continually in subduction zones to ≈700 km. The expected healing effects of pressure and temperature and growing amounts of seismic and experimental data suggest that earthquakes at depth probably represent self-organized failure analogous to, but different from, brittle failure. The only high-pressure shearing instabilities identified by experiment require generation
in situ
of a small fraction of very weak material differing significantly in density from the parent material. This “fluid” spontaneously forms mode I microcracks or microanticracks that self-organize via the elastic strain fields at their tips, leading to shear failure. Growing evidence suggests that the great majority of subduction zone earthquakes shallower than 400 km are initiated by breakdown of hydrous phases and that deeper ones probably initiate as a shearing instability associated with breakdown of metastable olivine to its higher-pressure polymorphs. In either case, fault propagation could be enhanced by shear heating, just as is sometimes the case with frictional sliding in the crust. Extensive seismological interrogation of the region of the Tonga subduction zone in the southwest Pacific Ocean provides evidence suggesting significant metastable olivine, with implication for its presence in other regions of deep seismicity. If metastable olivine is confirmed, either current thermal models of subducting slabs are too warm or published kinetics of olivine breakdown reactions are too fast.
Population structure of
Pseudomonas aeruginosa
Authors: Wiehlmann Lutz , Wagner Gerd , Cramer Nina , Siebert Benny , Gudowius Peter , Morales Gracia , Köhler Thilo , van Delden Christian , Weinel Christian , Slickers Peter , Tümmler Burkhard
Published: April 2007

The metabolically versatile Gram-negative bacterium
Pseudomonas aeruginosa
inhabits terrestrial, aquatic, animal-, human-, and plant-host-associated environments and is an important causative agent of nosocomial infections, particularly in intensive-care units. The population genetics of
P. aeruginosa
was investigated by an approach that is generally applicable to the rapid, robust, and informative genotyping of bacteria. DNA, amplified from the bacterial colony by circles of multiplex primer extension, is hybridized onto a microarray to yield an electronically portable binary multimarker genotype that represents the core genome by single nucleotide polymorphisms and the accessory genome by markers of genomic islets and islands. The 240 typed
P. aeruginosa
strains of diverse habitats and geographic origin segregated into two large nonoverlapping clusters and 45 isolated clonal complexes with few or no partners. The majority of strains belonged to few dominant clones widespread in disease and environmental habitats. The most frequent genotype was represented by the sequenced strain PA14. Core and accessory genome were found to be nonrandomly assembled in
P. aeruginosa
. Individual clones preferred a specific repertoire of accessory segments. Even the most promiscuous genomic island, pKLC102, had integrated preferentially into a subset of clones. Moreover, some physically distant loci of the core genome, including
oriC
, showed nonrandom associations of genotypes, whereas other segments in between were freely recombining. Thus, the
P. aeruginosa
genome is made up of clone-typical segments in core and accessory genome and of blocks in the core with unrestricted gene flow in the population.
Specificity in protein interactions and its relationship with sequence diversity and coevolution
Authors: Hakes Luke , Lovell Simon C. , Oliver Stephen G. , Robertson David L.
Published: April 2007

Studies of interacting proteins have found correlated evolution of the sequences of binding partners, apparently as a result of compensating mutations to maintain specificity (i.e., molecular coevolution). Here, we analyze the coevolution of interacting proteins in yeast and demonstrate correlated evolution of binding partners in eukaryotes. Detailed investigation of this apparent coevolution, focusing on the proteins' surface and binding interface, surprisingly leads to no improvement in the correlation. We conclude that true coevolution, as characterized by compensatory mutations between binding partners, is unlikely to be chiefly responsible for the apparent correlated evolution. We postulate that the correlation between sequence alignments is simply due to interacting proteins being subject to similar constraints on their evolutionary rate. Because gene expression has a strong influence on evolutionary rate, and interacting proteins will tend to have similar levels of expression, we investigated this particular constraint. We found that the absolute expression level outperformed correlated evolution for predicting interacting protein partners. A correlation between sequence alignments could also be identified not only between pairs of proteins that physically interact but also between those that are merely functionally related (i.e., within the same protein complex). This indicates that the observed correlated evolution of interacting proteins is due to similar constraints on evolutionary rate and not coevolution.
Neural interactions between flicker-induced self-organized visual hallucinations and physical stimuli
Authors: Billock Vincent A. , Tsou Brian H.
Published: May 2007

Spontaneous pattern formation in cortical activity may have consequences for perception, but little is known about interactions between sensory-driven and self-organized cortical activity. To address this deficit, we explored the relationship between ordinary stimulus-controlled pattern perception and the autonomous hallucinatory geometrical pattern formation that occurs for unstructured visual stimulation (e.g., empty-field flicker). We found that flicker-induced hallucinations are biased by the presentation of adjacent geometrical stimuli; geometrical forms that map to cortical area V1 as orthogonal gratings are perceptually opponent in biasing hallucinations. Rotating fan blades and pulsating circular patterns are the most salient biased hallucinations. Apparent motion and fractal (1/
f
) noise are also effective in driving hallucinatory pattern formation (the latter is consistent with predictions of spatiotemporal pattern formation driven by stochastic resonance). The behavior of these percepts suggests that self-organized hallucinatory pattern formation in human vision is governed by the same cortical properties of localized processing, lateral inhibition, simultaneous contrast, and nonlinear retinotopic mapping that govern ordinary vision.
OLE RNA, an RNA motif that is highly conserved in several extremophilic bacteria, is a substrate for and can be regulated by RNase P RNA
Authors: Ko Jae-hyeong , Altman Sidney
Published: May 2007

OLE (ornate, large, and extremophilic) RNA is a noncoding RNA that is found in several extremophilic bacteria, including
Bacillus halodurans
. The function of OLE RNA has not been clarified. In this study, we found that RNase P cleaves OLE RNA and that the cleavage leads to a small reduction of expression of a downstream gene determined by analyses
in vitro
and
in vivo
. Under RNase P-deficient conditions, the amount of OLE RNA increased. Our results imply that RNase P could play a role in the regulation of gene expression in relation to conserved RNA motifs like OLE RNA as well as in riboswitches and operons.
Repression of thePDCD2gene by BCL6 and the implications for the pathogenesis of human B and T cell lymphomas
Authors: Baron Beverly W. , Zeleznik-Le Nancy , Baron Miriam J. , Theisler Catherine , Huo Dezheng , Krasowski Matthew D. , Thirman Michael J. , Baron Rebecca M. , Baron Joseph M.
Published: April 2007

The humanBCL6gene on chromosome 3 band q27, which encodes a transcriptional repressor, is implicated in the pathogenesis of human lymphomas, especially the diffuse large B-cell type. We previously identified the humanPDCD2(programmed cell death-2) gene as a target of BCL6 repression.PDCD2encodes a protein that is expressed in many human tissues, including lymphocytes, and is known to interact with corepressor complexes. We now show that BCL6 can bind directly to thePDCD2promoter, repressing its transcription. Knockdown of endogenous BCL6 in a human B cell lymphoma line by introduction of small interfering RNA duplexes increases PDCD2 protein expression. Furthermore, there is an inverse relationship between the expression levels of the BCL6 and PDCD2 proteins in the lymphoid tissues of mice overexpressing human BCL6 (high BCL6 levels, minimal PDCD2) and controls (minimal BCL6, high PDCD2) as well as in tissues examined from some human B and T cell lymphomas. These data confirmPDCD2as a target of BCL6 and support the concept that repression ofPDCD2by BCL6 is likely important in the pathogenesis of certain human lymphomas.
Drift and breakup of spiral waves in reaction–diffusion–mechanics systems
Authors: Panfilov A. V. , Keldermann R. H. , Nash M. P.
Published: April 2007

Rotating spiral waves organize excitation in various biological, physical, and chemical systems. They underpin a variety of important phenomena, such as cardiac arrhythmias, morphogenesis processes, and spatial patterns in chemical reactions. Important insights into spiral wave dynamics have been obtained from theoretical studies of the reaction–diffusion (RD) partial differential equations. However, most of these studies have ignored the fact that spiral wave rotation is often accompanied by substantial deformations of the medium. Here, we show that joint consideration of the RD equations with the equations of continuum mechanics for tissue deformations (RD–mechanics systems), yield important effects on spiral wave dynamics. We show that deformation can induce the breakup of spiral waves into complex spatiotemporal patterns. We also show that mechanics leads to spiral wave drift throughout the medium approaching dynamical attractors, which are determined by the parameters of the model and the size of the medium. We study mechanisms of these effects and discuss their applicability to the theory of cardiac arrhythmias. Overall, we demonstrate the importance of RD–mechanics systems for mathematics applied to life sciences.
Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy
Authors: Walther Kirstin A. , Gräter Frauke , Dougan Lorna , Badilla Carmen L. , Berne Bruce J. , Fernandez Julio M.
Published: May 2007

We unfold and extend single proteins at a high force and then linearly relax the force to probe their collapse mechanisms. We observe a large variability in the extent of their recoil. Although chain entropy makes a small contribution, we show that the observed variability results from hydrophobic interactions with randomly varying magnitude from protein to protein. This collapse mechanism is common to highly extended proteins, including nonfolding elastomeric proteins like PEVK from titin. Our observations explain the puzzling differences between the folding behavior of highly extended proteins, from those folding after chemical or thermal denaturation. Probing the collapse of highly extended proteins with force spectroscopy allows separation of the different driving forces in protein folding.
A role for noncoding transcription in activation of the yeast
PHO5
gene
Authors: Uhler Jay P. , Hertel Christina , Svejstrup Jesper Q.
Published: May 2007

Noncoding, or intergenic, transcription by RNA polymerase II (RNAPII) is remarkably widespread in eukaryotic organisms, but the effects of such transcription remain poorly understood. Here we show that noncoding transcription plays a role in activation, but not repression, of the
Saccharomyces cerevisiae PHO5
gene. Histone eviction from the
PHO5
promoter during activation occurs with normal kinetics even in the absence of the
PHO5
TATA box, showing that transcription of the gene itself is not required for promoter remodeling. Nevertheless, we find that mutations that impair transcript elongation by RNAPII affect the kinetics of histone eviction from the
PHO5
promoter. Most dramatically, inactivation of RNAPII itself abolishes eviction completely. Under repressing conditions, an ≈2.4-kb noncoding exosome-degraded transcript is detected that originates near the
PHO5
termination site and is transcribed in the antisense direction. Abrogation of this transcript delays chromatin remodeling and subsequent RNAPII recruitment to
PHO5
upon activation. We propose that noncoding transcription through positioned nucleosomes can enhance chromatin plasticity so that chromatin remodeling and activation of traversed genes occur in a timely manner.
Vascular endothelial growth factor can signal through platelet-derived growth factor receptors
Authors: Ball Stephen G. , Shuttleworth C. Adrian , Kielty Cay M.
Published: May 2007

Vascular endothelial growth factor (VEGF-A) is a crucial stimulator of vascular cell migration and proliferation. Using bone marrow–derived human adult mesenchymal stem cells (MSCs) that did not express VEGF receptors, we provide evidence that VEGF-A can stimulate platelet-derived growth factor receptors (PDGFRs), thereby regulating MSC migration and proliferation. VEGF-A binds to both PDGFRα and PDGFRβ and induces tyrosine phosphorylation that, when inhibited, results in attenuation of VEGF-A–induced MSC migration and proliferation. This mechanism was also shown to mediate human dermal fibroblast (HDF) migration. VEGF-A/PDGFR signaling has the potential to regulate vascular cell recruitment and proliferation during tissue regeneration and disease.
Hif-1α regulates differentiation of limb bud mesenchyme and joint development
Authors: Provot Sylvain , Zinyk Dawn , Gunes Yasemin , Kathri Richa , Le Quynh , Kronenberg Henry M. , Johnson Randall S. , Longaker Michael T. , Giaccia Amato J. , Schipani Ernestina
Published: May 2007

Recent evidence suggests that low oxygen tension (hypoxia) may control fetal development and differentiation. A crucial mediator of the adaptive response of cells to hypoxia is the transcription factor Hif-1α. In this study, we provide evidence that mesenchymal condensations that give origin to endochondral bones are hypoxic during fetal development, and we demonstrate that Hif-1α is expressed and transcriptionally active in limb bud mesenchyme and in mesenchymal condensations. To investigate the role of Hif-1α in mesenchymal condensations and in early chondrogenesis, we conditionally inactivated Hif-1α in limb bud mesenchyme using a Prx1 promoter-driven Cre transgenic mouse. Conditional knockout of Hif-1α in limb bud mesenchyme does not impair mesenchyme condensation, but alters the formation of the cartilaginous primordia. Late hypertrophic differentiation is also affected as a result of the delay in early chondrogenesis. In addition, mutant mice show a striking impairment of joint development. Our study demonstrates a crucial, and previously unrecognized, role of Hif-1α in early chondrogenesis and joint formation.
NF90 regulates inducible IL-2 gene expression in T cells
Authors: Shi Lingfang , Godfrey Wayne R. , Lin Joseph , Zhao Guohua , Kao Peter N.
Published: May 2007

Activation of T cells induces the production of T cell growth and survival factor interleukin (IL) 2. Regulatory T cells intrinsically fail to induce IL-2 expression upon activation and can suppress IL-2 production in conventional T cells. Thus, the control of IL-2 expression is critically important to T cell immune responses, yet the mechanisms remain incompletely understood. Nuclear factor (NF) 90 is a zinc-finger DNA- and double-stranded RNA-binding protein subunit that binds specifically to the antigen receptor response element (ARRE)/NF of activated T cells target sequence in the IL-2 proximal promoter. Inducible binding of NF90 to the IL-2 promoter in vivo is shown by chromatin immunoprecipitation. NF90 gene-targeted mice exhibit perinatal lethality. Compared with newborn NF90+/+ mice, newborn NF90−/− mice demonstrate severe impairment of IL-2 expression. Compared with wild-type cells, T cells deficient in NF90 are impaired in ARRE and IL-2 transcriptional activation and IL-2 mRNA stabilization. Fetal liver cells from NF90 gene-targeted mice were transplanted into irradiated adult recombination activating gene (RAG)–2−/− and IL-2Rγ−/− mice deficient in T cells, B cells, and natural killer cells. NF90+/+- and NF90−/−-RAG chimeric mice showed grossly normal repopulation of the thymus and spleen, but only NF90−/− T cells were severely impaired in IL-2 gene expression. Compared with littermates, NF90−/− RAG chimeric mice exhibited profound T cell lymphocytopenia in the peripheral circulation. Thus, NF90 regulates inducible IL-2 transcription, mRNA stability, and gene expression in T cells and represents a novel therapeutic target for the modulation of T cell immune responses.
GAzer: gene set analyzer
Authors: Kim Sang-Bae , Yang Sungjin , Kim Seon-Kyu , Kim Sang Cheol , Woo Hyun Goo , Volsky David J. , Kim Seon-Young , Chu In-Sun
Published: April 2007

Summary: Gene Set Analyzer (GAzer) is a web-based integrated gene set analysis tool covering previously reported parametric and non-parametric models. Based on a simulation test for the reported algorithms, we classified and implemented three main statistical methods consisting of the z-statistic, gene permutation and sample permutation for ten gene set categories including Gene Ontology (GO) for human, mouse, rat and yeast. This tool identifies significantly altered gene sets scored by z-statistics and P-values from the z-test or permutation test and provides q-values and Bonferroni P-values to correct multiple hypothesis testing. GAzer allows users to observe changes in expression of each gene in a gene set or to see the significance of the gene sets containing a gene(s) of interest, thus allowing interactive data analysis both at the gene and gene set level. Moreover, GAzer offers extensive annotation for each gene.

Availability: The GAzer gene set analyzer is freely available at http://integromics.kobic.re.kr/GAzer/

Contact: kimsy@kribb.re.kr and chu@kribb.re.kr

Supplementary information: This can be found on the web page (http://integromics.kobic.re.kr/GAzer/supplement.jsp)
Alignment of molecular networks by integer quadratic programming
Authors: Li Zhenping , Zhang Shihua , Wang Yong , Zhang Xiang-Sun , Chen Luonan
Published: April 2007

Motivation: With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden.

Results: In this article, to find the conserved substructures, we develop an efficient algorithm for aligning molecular networks based on both molecule similarity and architecture similarity, by using integer quadratic programming (IQP). Such an IQP can be relaxed into the corresponding quadratic programming (QP) which almost always ensures an integer solution, thereby making molecular network alignment tractable without any approximation. The proposed framework is very flexible and can be applied to many kinds of molecular networks including weighted and unweighted, directed and undirected networks with or without loops.

Availability: Matlab code and data are available from http://zhangroup.aporc.org/bioinfo/MNAligner or http://intelligent.eic.osaka-sandai.ac.jp/chenen/software/MNAligner, or upon request from authors.

Contact: zxs@amt.ac.cn, chen@eic.osaka-sandai.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
Virgibacillus olivae sp. nov., isolated from waste wash-water from processing of Spanish-style green olives
Authors: Quesada Teresa , Aguilera Margarita , Morillo José Antonio , Ramos-Cormenzana Alberto , Monteoliva-Sánchez Mercedes
Published: May 2007

Four bacterial strains (E308T, E5549, I3077 and N30129) were isolated from the residual wash-water produced during the processing of Spanish-style green table olives. The isolates were subjected to a polyphasic taxonomic study using phenotypic, phylogenetic and genotypic methods. The bacteria were Gram-positive, spore-forming rods. Moreover, they were heterotrophs that were able to utilize cellobiose, glucose, mannose and rhamnose as carbon sources. The G+C content of their genomic DNA ranged from 30.7 to 33.4 mol%. The major cellular fatty acids found in strain E308T were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. DNA–DNA hybridization shows 76.2–88.3 % relatedness among the four strains. The 16S rRNA gene sequence of isolate E308T shows that it belongs to the genus Virgibacillus, with the highest sequence similarity (99 %) to Virgibacillus marismortui 123T. However, phenotypic differences and DNA–DNA relatedness between strain E308T and V. marismortui ATCC 700626T of less than 47 % suggest the placement of these strains within a novel species of the genus Virgibacillus. The name Virgibacillus olivae sp. nov. is proposed, with strain E308T (=LMG 23503T=DSM 18098T) as the type strain.