bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel dosimetric phantom for quality assurance of volumetric modulated arc therapy
Authors: Létourneau Daniel , Publicover Julia , Kozelka Jakub , Moseley Douglas J. , Jaffray David A.
Published: April 2009

The objective of this work is to assess the suitability and performance of a new dosimeter system with a novel geometry for the quality assurance (QA) of volumetric modulated arc therapy (VMAT). The new dosimeter system consists of a hollow cylinder (15 and 25 cm inner and outer diameters) with 124 diodes embedded in the phantom's cylindrical wall forming four rings of detectors. For coplanar beams, the cylindrical geometry and the ring diode pattern offer the advantage of invariant perpendicular incidence on the beam central axis for any gantry angle and also have the benefit of increasing the detector density as both walls of the cylinder sample the beam. Other advantages include real‐time readout and reduced weight with the hollow phantom shape. A calibration method taking into account the variation in radiation sensitivity of the diodes as a function of gantry angle was developed and implemented. In this work, the new dosimeter system was used in integrating mode to perform composite dose measurements along the cylindrical surface supporting the diodes. The reproducibility of the dosimeter response and the angular dependence of the diodes were assessed using simple 6 MV photon static beams. The performance of the new dosimeter system for VMAT QA was then evaluated using VMAT plans designed for a head and neck, an abdominal sarcoma, and a prostate patient. These plans were optimized with 90 control points (CPs) and additional versions of each plan were generated by increasing the number of CPs to 180 and 360 using linear interpolation. The relative dose measured with the dosimeter system for the VMAT plans was compared to the corresponding TPS dose map in terms of relative dose difference and distance to agreement (DTA). The dosimeter system's sensitivity to gantry rotation offset and scaling errors as well as setup errors was also evaluated. For static beams, the dosimeter system offered good reproducibility and demonstrated small residual diode angular dependence after calibration. For VMAT deliveries, the agreement between measured and calculated doses was good with of the diodes satisfying 3% of or 2 mm DTA for the 180 CP plans. The phantom offered sufficient sensitivity for the detection of small gantry rotation offset (3°) and scaling errors (1°) as well as phantom setup errors of 1 mm, although the results were plan dependent. With its novel geometry, the dosimeter system was also able to experimentally demonstrate the discretization effect of the number of CPs used in the TPS to simulate a continuous arc. These results demonstrate the suitability of the new dosimeter system for the patient‐specific QA of VMAT plans and suggest that the dosimeter system can be an effective tool in the routine QA and commissioning of treatment machines capable of VMAT delivery and cone‐beam CT image guidance.
Exploration of the potential of liquid scintillators for real‐time 3D dosimetry of intensity modulated proton beams
Authors: Beddar Sam , Archambault Louis , Sahoo Narayan , Poenisch Falk , Chen George T. , Gillin Michael T. , Mohan Radhe
Published: April 2009

In this study, the authors investigated the feasibility of using a 3D liquid scintillator (LS) detector system for the verification and characterization of proton beams in real time for intensity and energy‐modulated proton therapy. A plastic tank filled with liquid scintillator was irradiated with pristine proton Bragg peaks. Scintillation light produced during the irradiation was measured with a CCD camera. Acquisition rates of 20 and 10 frames per second (fps) were used to image consecutive frame sequences. These measurements were then compared to ion chamber measurements and Monte Carlo simulations. The light distribution measured from the images acquired at rates of 20 and 10 fps have standard deviations of 1.1% and 0.7%, respectively, in the plateau region of the Bragg curve. Differences were seen between the raw LS signal and the ion chamber due to the quenching effects of the LS and due to the optical properties of the imaging system. The authors showed that this effect can be accounted for and corrected by Monte Carlo simulations. The liquid scintillator detector system has a good potential for performing fast proton beam verification and characterization.
Requirement of Polyphosphate by
Pseudomonas fluorescens
Pf0-1 for Competitive Fitness and Heat Tolerance in Laboratory Media and Sterile Soil
Authors: Silby Mark W. , Nicoll Julie S. , Levy Stuart B.
Published: April 2009

Knowledge of the genetic basis for bacterial survival and persistence in soil is a critical component in the development of successful biological control strategies and for understanding the ecological success of bacteria. We found a locus specifying polyphosphate kinase (
ppk
) and a nonpredicted antisense RNA (
iiv8
) in
Pseudomonas fluorescens
Pf0-1 to be necessary for optimal competitive fitness in LB broth culture and sterile loam soil. Pf0-1 lacking
ppk
and
iiv8
was more than 10-fold less competitive against wild-type Pf0-1 in sterile loam soil low in inorganic phosphate. Studies indicated that
ppk
, and not
iiv8
, was required for competitive fitness. No role for
iiv8
was identified. While a
ppk
and
iiv8
mutant of Pf0-1 did not have increased sensitivity to osmotic, oxidative, and acid stress, it was more sensitive to elevated temperatures in laboratory medium and during growth in sterile soil.
ppk
was shown to be part of the Pho regulon in
P. fluorescens
, being upregulated in response to a low external P
i
concentration. Of importance, overproduction of polyphosphate in the soil environment appears to be more deleterious than production of none at all. Our findings reveal a new role for polyphosphate (and the need for proper regulation of its production) in competitive fitness of
P. fluorescens
in laboratory and soil environments.
Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity
Authors: Davis James P. , Youssef Noha H. , Elshahed Mostafa S.
Published: April 2009

We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55°C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.
Archaeal Diversity and the Prevalence of
Crenarchaeota
in Salt Marsh Sediments
Authors: Nelson Katelyn A. , Moin Nicole S. , Bernhard Anne E.
Published: April 2009

Crenarchaeal 16S rRNA sequences constituted over 70% of the archaeal clones recovered from three salt marsh sites dominated by different grasses. Group I.1a
Crenarchaeota
dominated at two sites, while group I.3b
Crenarchaeota
sequences were most abundant at a third site. Abundances of 16S rRNA genes related to “
Candidatus
Nitrosopumilus maritimus” differed by site and sampling date.
Utilization of Mucus from the Coral
Acropora palmata
by the Pathogen
Serratia marcescens
and by Environmental and Coral Commensal Bacteria
Authors: Krediet Cory J. , Ritchie Kim B. , Cohen Matthew , Lipp Erin K. , Sutherland Kathryn Patterson , Teplitski Max
Published: April 2009

In recent years, diseases of corals caused by opportunistic pathogens have become widespread. How opportunistic pathogens establish on coral surfaces, interact with native microbiota, and cause disease is not yet clear. This study compared the utilization of coral mucus by coral-associated commensal bacteria (“
Photobacterium mandapamensis
” and
Halomonas meridiana
) and by opportunistic
Serratia marcescens
pathogens.
S. marcescens
PDL100 (a pathogen associated with white pox disease of
Acroporid
corals) grew to higher population densities on components of mucus from the host coral. In an in vitro coculture on mucus from
Acropora palmata
,
S. marcescens
PDL100 isolates outgrew coral isolates. The white pox pathogen did not differ from other bacteria in growth on mucus from a nonhost coral,
Montastraea faveolata.
The ability of
S. marcescens
to cause disease in acroporid corals may be due, at least in part, to the ability of strain PDL100 to build to higher population numbers within the mucus surface layer of its acroporid host. During growth on mucus from
A. palmata
, similar glycosidase activities were present in coral commensal bacteria, in
S. marcescens
PDL100, and in environmental and human isolates of
S. marcescens
. The temporal regulation of these activities during growth on mucus, however, was distinct in the isolates. During early stages of growth on mucus, enzymatic activities in
S. marcescens
PDL100 were most similar to those in coral commensals. After overnight incubation on mucus, enzymatic activities in a white pox pathogen were most similar to those in pathogenic
Serratia
strains isolated from human mucosal surfaces.
Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge
Authors: Wang Shufang , Xiao Xiang , Jiang Lijing , Peng Xiaotong , Zhou Huaiyang , Meng Jun , Wang Fengping
Published: April 2009

The abundance and diversity of archaeal ammonia monooxygenase subunit A (
amoA
) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal
amoA
sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments.
Identification of Promoters for Efficient Gene Expression inMagnetospirillum gryphiswaldense
Authors: Lang Claus , Pollithy Anna , Schüler Dirk
Published: April 2009

To develop an expression system for the magnetotactic bacteriumMagnetospirillum gryphiswaldense, we compared gene expression from the widely usedEscherichia coliPlacpromoter with that from known and predicted genuineM. gryphiswaldensepromoters. With the use of green fluorescent protein as a reporter, the highest expression level was observed with the magnetosomal PmamDCpromoter. We demonstrate that this promoter can be used for the expression of modified magnetosome proteins to generate “antibody-binding” magnetosomes.
An IcmF Family Protein, ImpL
M
, Is an Integral Inner Membrane Protein Interacting with ImpK
L
, and Its Walker A Motif Is Required for Type VI Secretion System-Mediated Hcp Secretion in
Agrobacterium tumefaciens
Authors: Ma Lay-Sun , Lin Jer-Sheng , Lai Erh-Min
Published: April 2009

An intracellular multiplication F (IcmF) family protein is a conserved component of a newly identified type VI secretion system (T6SS) encoded in many animal and plant-associated
Proteobacteria
. We have previously identified ImpL
M
, an IcmF family protein that is required for the secretion of the T6SS substrate hemolysin-coregulated protein (Hcp) from the plant-pathogenic bacterium
Agrobacterium tumefaciens
. In this study, we characterized the topology of ImpL
M
and the importance of its nucleotide-binding Walker A motif involved in Hcp secretion from
A. tumefaciens
. A combination of β-lactamase-green fluorescent protein fusion and biochemical fractionation analyses revealed that ImpL
M
is an integral polytopic inner membrane protein comprising three transmembrane domains bordered by an N-terminal domain facing the cytoplasm and a C-terminal domain exposed to the periplasm.

impL
M

mutants with substitutions or deletions in the Walker A motif failed to complement the

impL
M

deletion mutant for Hcp secretion, which provided evidence that ImpL
M
may bind and/or hydrolyze nucleoside triphosphates to mediate T6SS machine assembly and/or substrate secretion. Protein-protein interaction and protein stability analyses indicated that there is a physical interaction between ImpL
M
and another essential T6SS component, ImpK
L
. Topology and biochemical fractionation analyses suggested that ImpK
L
is an integral bitopic inner membrane protein with an N-terminal domain facing the cytoplasm and a C-terminal OmpA-like domain exposed to the periplasm. Further comprehensive yeast two-hybrid assays dissecting ImpL
M
-ImpK
L
interaction domains suggested that ImpL
M
interacts with ImpK
L
via the N-terminal cytoplasmic domains of the proteins. In conclusion, ImpL
M
interacts with ImpK
L
, and its Walker A motif is required for its function in mediation of Hcp secretion from
A. tumefaciens
.
A Novel Allele of
kaiA
Shortens the Circadian Period and Strengthens Interaction of Oscillator Components in the Cyanobacterium
Synechococcus elongatus
PCC 7942
Authors: Chen You , Kim Yong-Ick , Mackey Shannon R. , Holtman C. Kay , LiWang Andy , Golden Susan S.
Published: April 2009

The basic circadian oscillator of the unicellular fresh water cyanobacterium
Synechococcus elongatus
PCC 7942, the model organism for cyanobacterial circadian clocks, consists of only three protein components: KaiA, KaiB, and KaiC. These proteins, all of which are homomultimers, periodically interact to form large protein complexes with stoichiometries that depend on the phosphorylation state of KaiC. KaiA stimulates KaiC autophosphorylation through direct physical interactions. Screening a library of
S. elongatus
transposon mutants for circadian clock phenotypes uncovered an atypical short-period mutant that carries a
kaiA
insertion. Genetic and biochemical analyses showed that the short-period phenotype is caused by the truncation of KaiA by three amino acid residues at its C terminus. The disruption of a negative element upstream of the
kaiBC
promoter was another consequence of the insertion of the transposon; when not associated with a truncated
kaiA
allele, this mutation extended the circadian period. The circadian rhythm of KaiC phosphorylation was conserved in these mutants, but with some modifications in the rhythmic pattern of KaiC phosphorylation, such as the ratio of phosphorylated to unphosphorylated KaiC and the relative phase of the circadian phosphorylation peak. The results showed that there is no correlation between the phasing of the KaiC phosphorylation pattern and the rhythm of gene expression, measured as bioluminescence from luciferase reporter genes. The interaction between KaiC and the truncated KaiA was stronger than normal, as shown by fluorescence anisotropy analysis. Our data suggest that the KaiA-KaiC interaction and the circadian pattern of KaiC autophosphorylation are both important for determining the period, but not the relative phasing, of circadian rhythms in
S. elongatus
.
Role of Quorum Sensing in
Sinorhizobium meliloti
-Alfalfa Symbiosis
Authors: Gurich Nataliya , González Juan E.
Published: April 2009

The ExpR/Sin quorum-sensing system of the gram-negative soil bacterium
Sinorhizobium meliloti
plays an important role in the establishment of symbiosis with its host plant
Medicago sativa
. A mutant unable to produce autoinducer signal molecules (
sinI
) is deficient in its ability to invade the host, but paradoxically, a strain lacking the quorum-sensing transcriptional regulator ExpR is as efficient as the wild type. We compared the whole-genome expression profile of the wild-type strain with strains missing one of the quorum-sensing regulatory components to identify genes controlled by the ExpR/Sin system throughout the different phases of the bacterial growth cycle, as well as in planta. Our analyses revealed that ExpR is a highly versatile regulator with a unique ability to show different regulatory capabilities in the presence or absence of an autoinducer. In addition, this study provided us with insight into the plant invasion defect displayed by the autoinducer mutant. We also discovered that the ExpR/Sin quorum-sensing system is repressed after plant invasion. Therefore, quorum sensing plays a crucial role in the regulation of many cell functions that ensures the successful invasion of the host and is inactivated once symbiosis is established.
6-Pyruvoyltetrahydropterin Synthase Paralogs Replace the Folate Synthesis Enzyme Dihydroneopterin Aldolase in Diverse Bacteria
Authors: Pribat Anne , Jeanguenin Linda , Lara-Núñez Aurora , Ziemak Michael J. , Hyde John E. , de Crécy-Lagard Valérie , Hanson Andrew D.
Published: April 2009

Dihydroneopterin aldolase (FolB) catalyzes conversion of dihydroneopterin to 6-hydroxymethyldihydropterin (HMDHP) in the classical folate biosynthesis pathway. However,
folB
genes are missing from the genomes of certain bacteria from the phyla
Chloroflexi
,
Acidobacteria
,
Firmicutes
,
Planctomycetes
, and
Spirochaetes
. Almost all of these
folB
-deficient genomes contain an unusual paralog of the tetrahydrobiopterin synthesis enzyme 6-pyruvoyltetrahydropterin synthase (PTPS) in which a glutamate residue replaces or accompanies the catalytic cysteine. A similar PTPS paralog from the malaria parasite
Plasmodium falciparum
is known to form HMDHP from dihydroneopterin triphosphate in vitro and has been proposed to provide a bypass to the FolB step in vivo. Bacterial genes encoding PTPS-like proteins with active-site glutamate, cysteine, or both residues were accordingly tested together with the
P. falciparum
gene for complementation of the
Escherichia coli folB
mutation. The
P. falciparum
sequence and bacterial sequences with glutamate or glutamate plus cysteine were active; those with cysteine alone were not. These results demonstrate that PTPS paralogs with an active-site glutamate (designated PTPS-III proteins) can functionally replace FolB in vivo. Recombinant bacterial PTPS-III proteins, like the
P. falciparum
enzyme, mediated conversion of dihydroneopterin triphosphate to HMDHP, but other PTPS proteins did not. Neither PTPS-III nor other PTPS proteins exhibited significant dihydroneopterin aldolase activity. Phylogenetic analysis indicated that PTPS-III proteins may have arisen independently in various PTPS lineages. Consistent with this possibility, merely introducing a glutamate residue into the active site of a PTPS protein conferred incipient activity in the growth complementation assay, and replacing glutamate with alanine in a PTPS-III protein abolished complementation.
Characterization of theCorynebacterium glutamicumΔpimB′ ΔmgtADouble Deletion Mutant and the Role ofMycobacterium tuberculosisOrthologues Rv2188c and Rv0557 in Glycolipid Biosynthesis
Authors: Mishra Arun K. , Batt Sarah , Krumbach Karin , Eggeling Lothar , Besra Gurdyal S.
Published: April 2009

In this study, utilizing aCorynebacterium glutamicumΔpimB′ ΔmgtAdouble deletion mutant, we unequivocally assign the in vivo functions of Rv2188c as an Ac1PIM1:mannosyltransferase (originally termed PimB′Mt[Mycobacterium tuberculosisPimB′]) and Rv0557 as a GlcAGroAc2:mannosyltransferase (originally termed PimBMt), which we have reassigned as PimBMtand MgtAMt, respectively, inMycobacterium tuberculosis.
Characterization of a Serine/Threonine Kinase Involved in Virulence of
Staphylococcus aureus
Authors: Débarbouillé Michel , Dramsi Shaynoor , Dussurget Olivier , Nahori Marie-Anne , Vaganay Elisabeth , Jouvion Grégory , Cozzone Alain , Msadek Tarek , Duclos Bertrand
Published: April 2009

Staphylococcus aureus
is a common human cutaneous and nasal commensal and a major life-threatening pathogen. Adaptation to the different environments encountered inside and outside the host is a crucial requirement for survival and colonization. We identified and characterized a eukaryotic-like serine/threonine kinase with three predicted extracellular PASTA domains (SA1063, or Stk1) and its associated phosphatase (SA1062, or Stp1) in
S. aureus
. Biochemical analyses revealed that Stk1 displays autokinase activity on threonine and serine residues and is localized to the membrane. Stp1 is a cytoplasmic protein with manganese-dependent phosphatase activity toward phosphorylated Stk1. In-frame deletions of the
stk1
and
stp1
genes were constructed in
S. aureus
strain 8325-4. Phenotypic analyses of the mutants revealed reduced growth of the
stk1
mutant in RPMI 1640 defined medium that was restored when adenine was added to the medium. Furthermore, the
stk1
mutant displayed increased resistance to Triton X-100 and to fosfomycin, suggesting modifications in cell wall metabolism. The
stk1
mutant was tested for virulence in a mouse pyelonephritis model and found to be strongly reduced for survival in the kidneys (approximately 2-log-unit decrease) compared to the parental strain. Renal histopathological analyses showed severe inflammatory lesions in mice infected with the parental
S. aureus
SH1000 strain, whereas the Δ
stk1
mutant led to only minimal renal lesions. These results confirm the important role of Stk1 for full expression of
S. aureus
pathogenesis and suggest that phosphorylation levels controlled by
stk1
are essential in controlling bacterial survival within the host.
Autoimmune pancytopenia following combination chemotherapy for chronic lymphocytic leukaemia: Figure 1
Authors: MacCallum S , Groves M , Brass D , Cunningham J , Sales M , Gelly K , Tauro S
Published: April 2009

Autoimmune haemolysis or thrombocytopenia can complicate purine nucleoside monotherapy for chronic lymphocytic leukaemia (CLL), but Evans syndrome is rare. This is a report of the occurrence of pancytopenia secondary to a unique combination of red cell aplasia with autoimmune thrombocytopenia and neutropenia in a patient with CLL following treatment with fludarabine and cyclophosphamide. This case is unusual for the simultaneous targeting of three haemopoietic lineages by immune dysfunction following fludarabine and cyclophosphamide, which is a treatment regimen believed to reduce autoimmune haematological toxicity in CLL.
SYMBOLIC ONE-CLASS LEARNING FROM IMBALANCED DATASETS: APPLICATION IN MEDICAL DIAGNOSIS
Authors: MENA LUIS , GONZALEZ JESUS A.
Published: April 2009

When working with real-world applications we often find imbalanced datasets, those for which there exists a majority class with normal data and a minority class with abnormal or important data. In this work, we make an overview of the class imbalance problem; we review consequences, possible causes and existing strategies to cope with the inconveniences associated to this problem. As an effort to contribute to the solution of this problem, we propose a new rule induction algorithm named Rule Extraction for MEdical Diagnosis (REMED), as a symbolic one-class learning approach. For the evaluation of the proposed method, we use different medical diagnosis datasets taking into account quantitative metrics, comprehensibility, and reliability. We performed a comparison of REMED versus C4.5 and RIPPER combined with over-sampling and cost-sensitive strategies. This empirical analysis of the REMED algorithm showed it to be quantitatively competitive with C4.5 and RIPPER in terms of the area under the Receiver Operating Characteristic curve (AUC) and the geometric mean, but overcame them in terms of comprehensibility and reliability. Results of our experiments show that REMED generated rules systems with a larger degree of abstraction and patterns closer to well-known abnormal values associated to each considered medical dataset.
THE DEPENDENCE OF LUMINOUS RED GALAXY (LRG) LUMINOSITY ON THE ENVIRONMENT
Authors: DENG XIN-FA , HE JI-ZHOU , WEN XIAO-QING , LUO CHENG-HONG
Published: April 2009

In order to investigate the dependence of LRG luminosity on the environment, we compare the luminosity distribution of member galaxies of LRG groups with that of isolated LRGs. It turns out that luminous LRGs exist preferentially in the densest regions of the universe (e.g. in groups), but faint LRGs are located preferentially in low density regions. The level of significance is above 2σ. This further confirms the dependence of galaxy luminosity on the environment.
CARTER'S CONSTANT REVEALED
Authors: ROSQUIST K. , BYLUND T. , SAMUELSSON L.
Published: April 2009

A new formulation of Carter's constant for geodesic motion in Kerr black holes is given. It is shown that Carter's constant corresponds to the total angular momentum plus a precisely defined part which is quadratic in the linear momenta. The characterization is exact in the weak field limit obtained by letting the gravitational constant go to zero. It is suggested that the new form can be useful in current studies of the dynamics of extreme mass ratio inspiral (EMRI) systems emitting gravitational radiation.
OPTICS OF SPIN-1 PARTICLES FROM GRAVITY-INDUCED PHASES
Authors: PAPINI G. , SCARPETTA G. , FEOLI A. , LAMBIASE G.
Published: April 2009

The Maxwell and Maxwell–de Rham equations can be solved exactly to first order in an external gravitational field. The gravitational background induces phases in the wave functions of spin-1 particles. These phases yield the optics of the particles without requiring any thin lens approximation.
UNDERSTANDING THE VERY-HIGH-ENERGY EMISSION FROM MICROQUASARS
Authors: BOSCH-RAMON VALENTÍ , KHANGULYAN DMITRY
Published: April 2009

Microquasars are X-ray binaries with relativistic jets. These jets are powerful energy carriers — thought to be fed by accretion — which produce nonthermal emission at different energy bands. The processes behind the bulk of the nonthermal emission in microquasars may be of leptonic (synchrotron and inverse Compton) and hadronic (proton–proton interactions, photomeson production, and photodisintegration) nature. When leptonic, the fast particle cooling would allow one to obtain relevant information about the properties close to the accelerator, like the radiation and the magnetic field energy densities, and the acceleration efficiency. When hadronic, the extreme conditions required in the emitter would have strong implications for the physics of jets and their surroundings. The very-high-energy part of the spectrum, i.e. > 100 GeV, is a good energy range to explore the physics behind the nonthermal radiation in these compact variable sources. In addition, this energy range, when taken together with lower energy bands, is a key piece for constructing a comprehensive picture of the processes occurring in the emitter. Until recently, the very-high-energy range was hard to probe due to the lack of sensitivity and spatial and spectral resolution of previous instrumentation. Nowadays, however, powerful gamma-ray instruments are operating and the quality of their observations is allowing one, for the first time, to start to understand the production of high-energy emission in microquasars.

To date, several galactic sources showing extended radio emission — among them at least one confirmed microquasar, Cygnus X-1 — have shown a TeV signal. All of them show complex patterns of spectral and temporal behavior. In this work, we discuss the physics behind the very-high-energy emission in Cygnus X-1, and also in the other two TeV binaries with detected extended outflows, LS 5039 and LS I +61 303, pointing out relevant aspects of the complex phenomena occurring in them. We conclude that the TeV emission is likely of leptonic origin, although hadrons cannot be discarded. In addition, efficient electromagnetic cascades can hardly develop since even relatively low magnetic fields suppress them. Also, the modeling of the radiation from some of the detected sources points to them as extremely efficient accelerators and/or having the TeV emitter at a distance from the compact object of about ~ 1012 cm. Finally, we point out that the role of a massive and hot stellar companion, due to its strong photon field and wind, cannot be neglected when trying to understand the behavior of microquasars at high and very high energies. The complexity of microquasars precludes straightforward generalizations to a whole population, and are better studied presently on a source-by-source basis. The new and future gamma-ray instrumentation will imply a big step further in our understanding of the processes in microquasars and gamma-ray-emitting binaries.
AN ECO-EPIDEMIOLOGICAL STUDY WITH PARASITE ATTACK AND ALTERNATIVE PREY
Authors: MANDAL A. K. , KUNDU KUSUMIKA , CHATTERJEE P. , CHATTOPADHYAY J.
Published: April 2009

The present paper deals with the problem of a predator-prey system with disease in the prey population. We observe the dynamics of such a system under the influence of severe as well as unnoticeable parasite attack and also alternative food sources for predator population. We assume the predator population will prefer only infected population for their diet as those are more vulnerable. Local and global stability of the system around the biological feasible equilibria are studied. The conditions for which all three species will persist are worked out. Our results indicate that in the case of severe parasite attack, the predator population will prefer the alternative food source and not the infected one. But the strategy is reversed in the case of unnoticeable parasite attack.
DISCRETE TIME SI AND SIS EPIDEMIC MODELS WITH VERTICAL TRANSMISSION
Authors: ZHANG JUPING , JIN ZHEN
Published: April 2009

Discrete time SI and SIS epidemic models with vertical transmission are presented in this paper. With regard to the SI model with constant or variable population size, we introduce an epidemic threshold parameter, the basic reproductive number R0, for predicting disease dynamics. R0 > 1 implies that the disease tends to an endemic equilibrium, while R0 < 1 implies disease extinction. On the other hand, for the SIS epidemic model with another form force of infection, the basic reproduction number R0 determines the persistence or extinction of the disease. In the same time, we also explore the relationship between the demographic equation and the epidemic process. In particular, we show that the epidemic model can exhibit bistability (alternative stable equilibria) over a wide range of parameter values.
TRAVELING PATTERN INDUCED BY MIGRATION IN AN EPIDEMIC MODEL
Authors: LI LI , SUN GUI-QUAN , JIN ZHEN
Published: April 2009

The main work in spatial epidemiology is the study of spatial variation in disease risk or incidence, including the spatial patterns of the populations. Spread of diseases in human populations can exhibit different patterns for spatially explicit approaches. In this paper, we investigate an epidemic model with both diffusion and migration. In the previous work (Sun et al., J Stat Mech P11011, 2007), we studied the model only with diffusion and obtained stationary Turing pattern. However, combined with migration, the model will exhibit typical traveling pattern, which is shown by both mathematical analysis and numerical simulations. The results obtained well extend the finding of pattern formation in the epidemic model and may well explain the field observed in the real world.
HIGHLIGHTING RELATIONSHIPS BETWEEN HETEROGENEOUS BIOLOGICAL DATA THROUGH GRAPHICAL DISPLAYS BASED ON REGULARIZED CANONICAL CORRELATION ANALYSIS
Authors: GONZÁLEZ I. , DÉJEAN S. , MARTIN P. G. P. , GONÇALVES O. , BESSE P. , BACCINI A.
Published: April 2009

Biological data produced by high throughput technologies are becoming more and more abundant and are arousing many statistical questions. This paper addresses one of them; when gene expression data are jointly observed with other variables with the purpose of highlighting significant relationships between gene expression and these other variables. One relevant statistical method to explore these relationships is Canonical Correlation Analysis (CCA). Unfortunately, in the context of postgenomic data, the number of variables (gene expressions) is usually greater than the number of units (samples) and CCA cannot be directly performed: a regularized version is required.

We applied regularized CCA on data sets from two different studies and show that its interpretation evidences both previously validated relationships and new hypothesis. From the first data sets (nutrigenomic study), we generated interesting hypothesis on the transcription factor pathways potentially linking hepatic fatty acids and gene expression. From the second data sets (pharmacogenomic study on the NCI-60 cancer cell line panel), we identified new ABC transporter candidate substrates which relevancy is illustrated by the concomitant identification of several known substrates.

In conclusion, the use of regularized CCA is likely to be relevant to a number and a variety of biological experiments involving the generation of high throughput data. We demonstrated here its ability to enhance the range of relevant conclusions that can be drawn from these relatively expensive experiments.
IMPLIED VOLATILITY FROM ASIAN OPTIONS VIA MONTE CARLO METHODS
Authors: YANG ZHAOJUN , EWALD CHRISTIAN-OLIVER , XIAO YAJUN
Published: April 2009

We discuss how implied volatilities for OTC traded Asian options can be computed by combining Monte Carlo techniques with the Newton method in order to solve nonlinear equations. The method relies on accurate and fast computation of the corresponding vegas of the option. In order to achieve this we propose the use of logarithmic derivatives instead of the classical approach. Our simulations document that the proposed method shows far better results than the classical approach. Furthermore we demonstrate how numerical results can be improved by localization.
PRICING FOR GEOMETRIC MARKED POINT PROCESSES UNDER PARTIAL INFORMATION: ENTROPY APPROACH
Authors: CECI CLAUDIA , GERARDI ANNA
Published: April 2009

The problem of the arbitrage-free pricing of a European contingent claim B is considered in a general model for intraday stock price movements in the case of partial information. The dynamics of the risky asset price is described through a marked point process Y, whose local characteristics depend on some unobservable jump diffusion process X. The processes Y and X may have common jump times, which means that the trading activity may affect the law of X and could be also related to the presence of catastrophic events. Risk-neutral measures are characterized and in particular, the minimal entropy martingale measure is studied. The problem of pricing under restricted information is discussed, and the arbitrage-free price of the claim B w.r.t. the minimal entropy martingale measure is computed by using filtering techniques.
REGIME-SWITCHED VOLATILITY OF BRENT CRUDE OIL FUTURES WITH MARKOV-SWITCHING ARCH MODEL
Authors: CHIU TIEN-YU , SHIEH SHWU-JANE
Published: April 2009

This paper investigates the volatility process of the Brent crude oil futures markets using Markov-switching ARCH (SWARCH) model. The SWARCH model allows the conditional disturbances to change as time passes and even to switch in different regimes. The empirical evidence shows that the SWARCH (3,3) model performs the best goodness of fit and the best forecast performance among different fitting models. The estimation of smoothing probabilities of data under different regimes facilitates to capture the characteristics of the data, and the high-volatility regime is associated with some extraordinary events, such as the 1990's Persian Gulf War, the 1997's Asia Financial Crisis, and the 2001's 911 terrorist attack.
A "COHERENT STATE TRANSFORM" APPROACH TO DERIVATIVE PRICING
Authors: PERISSINOTTO LUDOVICO , TEBALDI CLAUDIO
Published: April 2009

We propose an extension of the transform approach to option pricing introduced in Duffie, Pan and Singleton (Econometrica68(6) (2000) 1343–1376) and in Carr and Madan (Journal of Computational Finance2(4) (1999) 61–73). We term this extension the "coherent state transform" approach, it applies when the Markov generator of the factor process can be decomposed as a linear combination of generators of a Lie symmetry group. Then the family of group invariant coherent states determine the transform to price derivatives. We exemplify this procedure deriving a coherent state transform for affine jump-diffusion processes with positive state space. It improves the traditional FFT because inversion of the latter requires integration over an unbounded domain, while inversion of the coherent state transform requires integration over unit ball. We explicitly perform the pricing exercise for some contracts like the plain vanilla options on (credit) risky bonds and on the spread option.
The Polar Deposits of Mars
Authors: Byrne Shane
Published: April 2009

The tantalizing prospect of a readable record of martian climatic variations has driven decades of work toward deciphering the stratigraphy of the martian polar layered deposits and understanding the role of the residual ice caps that cover them. Spacecraft over the past decade have provided a massive infusion of new data into Mars science. Polar science has benefited immensely due to the near-polar orbits of most of the orbiting missions and the successful landing of the Phoenix spacecraft in the northern high latitudes. Topographic, thermal, radar, hyperspectral, and high-resolution imaging data are among the datasets that have allowed characterization of the stratigraphy of the polar layered deposits in unprecedented detail. Additionally, change within the residual ice caps has been monitored with spacecraft instruments for several years. These new data have provided a golden opportunity to understand the interplay between the martian orbit, climate, and polar ice.
Planetary Migration: What Does It Mean for Planet Formation?
Authors: Chambers John E.
Published: April 2009

Gravitational interactions between a planet and its protoplanetary disk change the planet's orbit, causing the planet to migrate toward or away from its star. Migration rates are poorly constrained for low-mass bodies but reasonably well understood for giant planets. In both cases, significant migration will affect the details and efficiency of planet formation. If the disk is turbulent, density fluctuations will excite orbital eccentricities and cause orbits to undergo a random walk. Both processes are probably detrimental to planet formation. Planets that form early in the lifetime of a disk are likely to be lost, whereas late-forming planets will survive and may undergo little migration. Migration can explain the observed orbits and masses of extrasolar planets if giants form at different times and over a range of distances. Migration can also explain the existence of planets orbiting close to their star and of resonant pairs of planets.
Evolution of the Genus Homo
Authors: Tattersall Ian , Schwartz Jeffrey H.
Published: April 2009

Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the ∼2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis. We also point to heterogeneity among “early African Homo erectus,” and the lack of apomorphies linking these fossils to the Asian Homo erectus group, a cohesive regional clade that shows some internal variation, including brain size increase over time. The first truly cosmopolitan Homo species is Homo heidelbergensis, known from Africa, Europe, and China following 600 kyr ago. One species sympatric with it included the >500-kyr-old Sima de los Huesos fossils from Spain, clearly distinct from Homo heidelbergensis and the oldest hominids assignable to the clade additionally containing Homo neanderthalensis. This clade also shows evidence of brain size expansion with time; but although Homo neanderthalensis had a large brain, it left no unequivocal evidence of the symbolic consciousness that makes our species unique. Homo sapiens clearly originated in Africa, where it existed as a physical entity before it began (also in that continent) to show the first stirrings of symbolism. Most likely, the biological underpinnings of symbolic consciousness were exaptively acquired in the radical developmental reorganization that gave rise to the highly characteristic osteological structure of Homo sapiens, but lay fallow for tens of thousands of years before being “discovered” by a cultural stimulus, plausibly the invention of language.
The Channeled Scabland: A Retrospective
Authors: Baker Victor R.
Published: April 2009

The Channeled Scabland of east-central Washington in the United States is a complex of anastomosing rock-cut fluvial channels, cataracts, loess islands, rock basins, broad gravel deposits, and immense gravel bars. In the 1920s, J Harlen Bretz demonstrated that the Channeled Scabland formed by cataclysmic erosion and deposition from Pleistocene megaflooding derived from the margins of the Cordilleran Ice Sheet, particularly glacial Lake Missoula in western Montana and northern Idaho. Studies of this region and the high-energy flood processes that generated it are stimulating (a) discoveries of similar megaflood-related landscapes around the world and on Mars, (b) enhanced understanding of the processes involved in the fluvial erosion of bedrock, and (c) the use of paleoflood indicators for understanding the magnitudes and frequency of flooding.
Fenofibrate inhibits aldosterone-induced apoptosis in adult rat ventricular myocytes via stress-activated kinase-dependent mechanisms
Authors: De Silva Deepa S. , Wilson Richard M. , Hutchinson Christoph , Ip Peter C. , Garcia Anthony G. , Lancel Steve , Ito Masa , Pimentel David R. , Sam Flora
Published: April 2009

Aldosterone induces extracellular signal-regulated kinase (ERK)-dependent cardiac remodeling. Fenofibrate improves cardiac remodeling in adult rat ventricular myocytes (ARVM) partly via inhibition of aldosterone-induced ERK1/2 phosphorylation and inhibition of matrix metalloproteinases. We sought to determine whether aldosterone caused apoptosis in cultured ARVM and whether fenofibrate ameliorated the apoptosis. Aldosterone (1 μM) induced apoptosis by increasing terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL)-positive nuclei in ARVM. Spironolactone (100 nM), an aldosterone receptor antagonist, but not RU-486, a glucocorticoid receptor, inhibited aldosterone-mediated apoptosis, indicating that the mineralocorticoid receptor (MR) plays a role. SP-600125 (3 μM)—a selective inhibitor of c-Jun NH2-terminal kinase (JNK)—inhibited aldosterone-induced apoptosis in ARVM. Although aldosterone increased the expression of both stress-activated protein kinases, pretreatment with fenofibrate (10 μM) decreased aldosterone-mediated apoptosis by inhibiting only JNK phosphorylation and the aldosterone-induced increases in Bax, p53, and cleaved caspase-3 and decreases in Bcl-2 protein expression in ARVM. In vivo studies demonstrated that chronic fenofibrate (100 mg·kg body wt−1·day−1) inhibited myocardial Bax and increased Bcl-2 expression in aldosterone-induced cardiac hypertrophy. Similarly, eplerenone, a selective MR inhibitor, used in chronic pressure-overload ascending aortic constriction inhibited myocardial Bax expression but had no effect on Bcl-2 expression. Therefore, involvement of JNK MAPK-dependent mitochondrial death pathway mediates ARVM aldosterone-induced apoptosis and is inhibited by fenofibrate, a peroxisome proliferator-activated receptor (PPAR)α ligand. Fenofibrate mediates beneficial effects in cardiac remodeling by inhibiting programmed cell death and the stress-activated kinases.
β-Adrenergic regulation of a novel isoform of NCX: sequence and expression of shark heart NCX in human kidney cells
Authors: Janowski Einsley , Day Regina , Kraev Alexander , Roder John C. , Cleemann Lars , Morad Martin
Published: April 2009

The function, regulation, and molecular structure of the cardiac Na+/Ca2+exchangers (NCXs) vary significantly among vertebrates. We previously reported that β-adrenergic suppression of amphibian cardiac NCX1.1 is associated with specific molecular motifs. Here we investigated the bimodal, cAMP-dependent regulation of spiny dogfish shark ( Squalus acanthias) cardiac NCX, exploring the effects of molecular structure, host cell environment, and ionic milieu. The shark cardiac NCX sequence (GenBank accession no. DQ068478 ) revealed two novel proline/alanine-rich amino acid insertions. Wild-type and mutant shark NCXs were cloned and expressed in mammalian cells (HEK-293 and FlpIn-293), where their activities were measured as Ni2+-sensitive Ca2+fluxes (fluo 4) and membrane (Na+/Ca2+exchange) currents evoked by changes in extracellular Na+concentration and/or membrane potential. Regardless of Ca2+buffering, β-adrenergic stimulation of cloned wild-type shark NCX consistently produced bimodal regulation (defined as differential regulation of Ca2+-efflux and -influx pathways), with suppression of the Ca2+-influx mode and either no change or enhancement of the Ca2+-efflux mode, closely resembling results from parallel experiments with native shark cardiomyocytes. In contrast, mutant shark NCX, with deletion of the novel region 2 insertion, produced equal suppression of the inward and outward currents and Ca2+fluxes, thereby abolishing the bimodal nature of the regulation. Control experiments with nontransfected and dog cardiac NCX-expressing cells showed no cAMP regulation. We conclude that bimodal β-adrenergic regulation is retained in cloned shark NCX and is dependent on the shark's unique molecular motifs.