bluuebunny/crossref_metadata_2025 huggingface dataset:
Using GPUs for Realtime Prediction of Optical Forces on Microsphere Ensembles
Authors: Bista Sujal , Chowdhury Sagar , Gupta Satyandra K. , Varshney Amitabh
Published: April 2013

Laser beams can be used to create optical traps that can hold and transport small particles. Optical trapping has been used in a number of applications ranging from prototyping at the microscale to biological cell manipulation. Successfully using optical tweezers requires predicting optical forces on the particle being trapped and transported. Reasonably accurate theory and computational models exist for predicting optical forces on a single particle in the close vicinity of a Gaussian laser beam. However, in practice the workspace includes multiple particles that are manipulated using individual optical traps. It has been experimentally shown that the presence of a particle can cast a shadow on a nearby particle and hence affect the optical forces acting on it. Computing optical forces in the presence of shadows in real-time is not feasible on CPUs. In this paper, we introduce a ray-tracing-based application optimized for GPUs to calculate forces exerted by the laser beams on microparticle ensembles in an optical tweezers system. When evaluating the force exerted by a laser beam on 32 interacting particles, our GPU-based approach is able to get a 66-fold speed up compared to a single core CPU implementation of traditional Ashkin's approach and a 10-fold speedup over the single core CPU-based implementation of our approach.
Emerging Design Methods and Tools in Collaborative Product Development
Authors: Red Edward , French David , Jensen Gregory , Walker Sheli Sillito , Madsen Peter
Published: April 2013

Product development uses the engineering design process to conceptualize and design new products, while relying on computer-aided application tools like CAD/CAE/CAM that are unfortunately designed for single users. In the absence of multiuser engineering applications, this paper uses surveys and facility visits to show an increased reliance on social communication tools for closing design collaboration feedback loops. Product development requires collaboration among myriad personnel and organizations, each having unique complementary experiences and capabilities. Collaborative design has a primary goal: reduce time-to-market and competitive costs for new products, while retaining quality of product performance and minimizing environmental impact. The focus of this paper is to compare contemporary methods and tools used in collaborative product design at notable corporations to emerging multiuser computer-aided applications. This comparison will define a future where design mistakes and time-to-market are reduced, collaboration is not only truly concurrent, but simultaneously concurrent, and where design rationale is more easily captured and shared for later review and for educational training.
Temperature and Pressure Effects on Hydrogen Separation From Syngas
Authors: Leyko Aaron B. , Gupta Ashwani K.
Published: April 2013

Multicomponent synthetic gas (syngas) mixtures produced from the gasification of coal, low grade fuel, wastes, and biomass offers a novel source of hydrogen production. Gasification also eliminates much of the pollutant emissions from the combustion these fuels. Palladium based membranes offer a promising method for extracting hydrogen from syngas. Experimental results are presented from a laboratory scale experimental facility. This facility was designed and built to examine various types of palladium and palladium alloy membranes for harvesting hydrogen from the syngas. The thin membranes (on the order of ∼12 μm) examined were supported on porous stainless-steel. A mixture of pure gasses consisting of hydrogen, nitrogen, and carbon dioxide were used to simulate syngas of different composition. The specific focus was on evaluating the role of operational temperature and pressure of membrane on the separation efficiency of hydrogen. Results are reported at temperatures from 325 °C to 400 °C and pressures from 5 to 30 psi (gauge) for various concentrations of hydrogen in the gas mixture. Results showed permeation to increase by up to 33% with a 75 °C increase in temperature. Permeation increased by over 50% with an increase in partial pressure of hydrogen by only 10 psi. These results provide clean hydrogen recovery from syngas obtained from gasification and pyrolysis of wastes and biomass.
Po‐Poster ‐ 12: Evaluation of MOSFETS for Gamma Knife® helmet factor measurements
Authors: Kurjewicz L , Berndt A
Published: April 2013

The Gamma Knife ® is calibrated annually using the 18 mm collimator helmet; the dose rates for the other helmets are determined by measuring the radiation output relative to the 18 mm helmet. These relative measurements yield a helmet factor for each collimator helmet, which is incorporated into the treatment planning software, and is validated during annual quality assurance testing. Traditionally, helmet factors have been measured using 1×1×1 mm3 thermoluminescent dosimeters (TLDs). Determining helmet factors using this technique is a challenging process since the TLDs are small and fragile, and their preparation, calibration and readout is very time consuming. They also have a large uncertainty of 2 to 5%. The goal of this research is to investigate the use of metal oxide semiconductor field effect transistor dosimeters (MOSFETs) for Gamma Knife® helmet factor measurements. The MOSFET linearity and reproducibility was first characterized using a teletherapy unit; the linearity and reproducibility were both found to be within 2%. The helmet factors were then measured using TLDs, and again using MOSFETs. The TLD results gave helmet factors within 2.5% of the manufacturer's values; the MOSFETs provided helmet factors within 1.3% of the manufacturer's values, in a fraction of the time it took to generate the TLD results. This investigation confirms that MOSFETs can be used to measure Gamma Knife® helmet factors more quickly and accurately than TLDs.
Po‐Poster ‐ 14: In‐house leak testing with a multi‐channel analyzer system
Authors: Abdel‐Rahman W , Corns R , Evans M , Podgorsak E
Published: April 2013

The URSA‐II Multi‐Channel Analyzer (MCA) (URSA‐II Radiation Safety Associates, Inc. Hebron, CT) connected to a NaI well counter (PR‐4112, Ludlum Measurements, Inc. Sweetwater, TX) is an ideal instrument for performing accurate assays of samples with low levels of activity. Clinically this is important for assaying leak‐test samples taken from sealed sources. Leak testing is a Canadian Nuclear Safety Commission (CNSC) licensing requirement for all sealed sources with activities exceeding 50 MBq. The URSA‐II was evaluated by calibrating the system using a set of known Co‐60 and Cs‐137 sources and then assaying a second set of known Co‐60 and Cs‐137 test sources. The measured activities for the test sources set were within ±5% of the values listed on the certificate once corrected for decay. We found the minimum detectable activity (MDA) for this instrument is 7 Bq for Co‐60 and 3 Bq for Cs‐137 when using a fixed counting time of 60 seconds. These MDAs demonstrate this instrument would have no difficulties in determining if a leak test sample is under the 200 Bq action level as dictated by the CNSC in the CNSC regulatory document R‐116 for leak testing. The URSA‐II is a convenient and simple tool for performing in‐house leak testing as part of a standard license compliance program for class II clinical installations.
Po‐Poster ‐ 19: Local minima in anatomic aperture‐based IMRT optimization
Authors: Aubry J , Beaulieu F , Beaulieu L , Tremblay D
Published: April 2013

Purpose: An anatomic aperture‐based IMRT optimization program, named Ballista, was developed at our institution. Even though studies previously published concluded local minima in full‐IMRT optimization were not problematic, early observations with Ballista revealed their nuisance. The purpose of the present study was to evaluate the extent of local minima and their impact on the optimization. Method and Materials: In Ballista beam weights are optimized by quasi‐Newton algorithm, which cannot escape local minima, even with a quadratic dose‐based objective function. Therefore, a large number of descents were launched with random initial weights to explore the solution space for a varying number of beams. Treatment plan DVHs of different local minima were also analyzed. Results: When four beam weights were optimized, only a few but very distinctive local minima were found. For a case of 20 beam weights, the optimization revealed an astonishing number of local minima. DVH analysis showed local minima generally favor one or more organs‐at‐risk (OARs) while the other objectives are less than optimal compared with the global minimum. It was found that limiting the initial beam weights to small values eliminates the majority of the solution space containing local minima. Conclusion: With Ballista local minima proved to be a major problem. Plans corresponding to different minima differed drastically. In order to give the optimization a “clear shot” at the global minimum, initial beam weights must be limited to small values. The optimization thus focuses on improving the target volume objectives since all OARs objectives are initially met.
Po‐Poster ‐ 24: A new tool to perform the timing alignment of the detectors in a PET scanner
Authors: Thompson C , St. James S
Published: April 2013

Timing alignment of the detectors in a PET Scanner is important in order to reduce the random counts with a major source of image noise in 3D whole body scans used in the evaluation of cancer patients. A new technique is described here and being tested on individual PET detectors at the Montreal Neurological Institute. A timing alignment probe manufactured by Scanwell Systems (Montreal, QC) uses a small quantity of Na‐22 embedded in plastic scintillator, which can detect each positron decay. The difference between the time of decay and time of gamma ray detection can be used to establish a time offset for each crystal in a PET Scanner. This paper reports the results from isolated PET detectors, since no PET Scanners presently have an input for the timing probe. We found that in fast detectors the timing alignment could be made with an accuracy of 120 ps in a ten minute scan for each crystal. Variations of up to 1.9 ns were observed from individual crystals from typical block detectors in conventional PET Scanners.
Po‐Poster ‐ 30: A method to estimate an exponential elastic model
Authors: Zhong H , Peters T
Published: April 2013

The response of soft tissue to interventional actions is an important subject in surgery simulation and planning. With properly calibrated elastic properties, it is possible to build a computational model to predict the deformation and stress of different organs. This paper studies the biomechanical properties of a pig liver and proposes a parameter evaluation method specifically for an exponential constitutive model
urn:x-wiley:00942405:media:mp1009:mp1009-math-0001 which is extensively used in the literature. Under the assumption of the incompressibility, the uniaxial deformation mode allows us to generate a simplified stress expression:
urn:x-wiley:00942405:media:mp1009:mp1009-math-0002 Different from a general trial and error procedure employed when constructing a finite element computational model, here we fit the above simplified stress expression with the experimental curve of stress and strain using a least square method. The fitted result shows that for a sample of a pig liver, b=8.6, C=0.000169 (N/mm2), and A=ln(bC)=−6.53. From the value A we also can deduce Young's module which satisfies E=6bC under a small strain. Consequently we determine that E=6eA=0.0088. We then compare the theoretic model with some published data, and find that the exponential model calibrated with this method matches well with both the Ogden model and an experimental result. Therefore the calibrated parameters could serve as a valuable reference in building a computational physics‐based deformable model for surgical simulation and radiation treatment planning.
Sci‐PM Fri ‐ 05: Effects of coating on friction force during needle insertion in soft materials
Authors: Podder T , Clark D , Fuller D , Sherman J , Messing E , Rubens D , Strang J , Ng W , Yu Y
Published: April 2013

Purpose: Of the three main forces, i.e. stiffness force, friction force and cutting force experienced during needle insertion in soft tissue/material, friction force contributes the major portion. Higher friction force is partly responsible for large deformation/displacement of soft tissues/organs during various medical diagnostic and therapeutic procedures. In this study we investigate the effectiveness of needle coating on friction force reduction. Methods and Materials: We have used three types of 18G brachytherapy needles, two of them coated with Teflon and Carbon. Then we have compared the results with standard commercial needle whose coating is unknown. Needles were inserted by a 6 DOF robotic system in soft material phantoms prepared from polyvinylchloride with 25% softener. A 6 DOF force sensor (Nano25®) was mounted on the end‐effector of the robot. To assess the friction force alone, the needle tips were passed through the phantom; only the cannulas were in contact with the material while the data were recorded. Results: We observed significant reduction, about 34% at both 5 & 100mm/s speed, in friction force on needle with Carbon coating. Some improvement was also noticed with Teflon coated needle, about 15% reduction at both 5 & 100mm/s speed. Discussions: Carbon coating is the most effective in reduction of friction force on the needle. Therefore, one of the solutions to reduce tissue/organ deformation/displacement may be coating surgical needles with Carbon. However, chemical and pathological studies are required before going for clinical trials with Carbon coated needles. Acknowledgement: Work supported by NCI grant R01 CA091763.
Structural Analysis of the Role of Pseudomonas aeruginosa Penicillin-Binding Protein 5 in β-Lactam Resistance
Authors: Smith Jeffrey D. , Kumarasiri Malika , Zhang Weilie , Hesek Dusan , Lee Mijoon , Toth Marta , Vakulenko Sergei , Fisher Jed F. , Mobashery Shahriar , Chen Yu
Published: April 2013

Penicillin-binding protein 5 (PBP5) is one of the most abundant PBPs in
Pseudomonas aeruginosa
. Although its main function is that of a cell wall
dd
-carboxypeptidase, it possesses sufficient β-lactamase activity to contribute to the ability of
P. aeruginosa
to resist the antibiotic activity of the β-lactams. The study of these dual activities is important for understanding the mechanisms of antibiotic resistance by
P. aeruginosa
, an important human pathogen, and to the understanding of the evolution of β-lactamase activity from the PBP enzymes. We purified a soluble version of
P. aeruginosa
PBP5 (designated Pa sPBP5) by deletion of its C-terminal membrane anchor. Under
in vitro
conditions, Pa sPBP5 demonstrates both
dd
-carboxypeptidase and expanded-spectrum β-lactamase activities. Its crystal structure at a 2.05-Å resolution shows features closely resembling those of the class A β-lactamases, including a shortened loop spanning residues 74 to 78 near the active site and with respect to the conformations adopted by two active-site residues, Ser101 and Lys203. These features are absent in the related PBP5 of
Escherichia coli
. A comparison of the two Pa sPBP5 monomers in the asymmetric unit, together with molecular dynamics simulations, revealed an active-site flexibility that may explain its carbapenemase activity, a function that is absent in the
E. coli
PBP5 enzyme. Our functional and structural characterizations underscore the versatility of this PBP5 in contributing to the β-lactam resistance of
P. aeruginosa
while highlighting how broader β-lactamase activity may be encoded in the structural folds shared by the PBP and serine β-lactamase classes.
Human Monoclonal Antibodies against Clostridium difficile Toxins A and B Inhibit Inflammatory and Histologic Responses to the Toxins in Human Colon and Peripheral Blood Monocytes
Authors: Koon Hon Wai , Shih David Q. , Hing Tressia C. , Yoo Jun Hwan , Ho Samantha , Chen Xinhua , Kelly Ciarán P. , Targan Stephan R. , Pothoulakis Charalabos
Published: April 2013

Clostridium difficileinfection (CDI) is a common and debilitating nosocomial infection with high morbidity and mortality.C. difficilemediates diarrhea and colitis by releasing two toxins, toxin A and toxin B. Since both toxins stimulate proinflammatory signaling pathways in human colonocytes and both are involved in the pathophysiology of CDI, neutralization of toxin A and B activities may represent an important therapeutic approach against CDI. Recent studies indicated that human monoclonal antibodies (MAbs) against toxins A and B reduce their cytotoxic and secretory activities and prevent CDI in hamsters. Moreover, anti-toxin A and anti-toxin B MAbs together with antibiotics also effectively reduced recurrent CDI in humans. However, whether these MAbs neutralize toxin A- and toxin B-associated immune responses in human colonic mucosa or human peripheral blood monocyte cells (PBMCs) has never been examined. We used fresh human colonic biopsy specimens and peripheral blood monocytes to evaluate the effects of these antibodies against toxin A- and B-associated cytokine release, proinflammatory signaling, and histologic damage. Incubation of anti-toxin A (MK3415) or anti-toxin B (MK6072) MAbs with human PBMCs significantly inhibited toxin A- and toxin B-mediated tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) expression. MK3415 and MK6072 also diminished toxin A- and toxin B-mediated NF-κB p65 phosphorylation in human monocytes, respectively, and significantly reduced toxin A- and B-induced TNF-α and IL-1β expression as well as histologic damage in human colonic explants. Our results underline the effectiveness of MK3415 and MK6072 in blockingC. difficiletoxin A- and toxin B-mediated inflammatory responses and histologic damage.
Borrelia burgdorferi bba66
Gene Inactivation Results in Attenuated Mouse Infection by Tick Transmission
Authors: Patton Toni G. , Brandt Kevin S. , Nolder Christi , Clifton Dawn R. , Carroll James A. , Gilmore Robert D.
Published: April 2013

The impact of the
Borrelia burgdorferi
surface-localized immunogenic lipoprotein BBA66 on vector and host infection was evaluated by inactivating the encoding gene,
bba66
, and characterizing the mutant phenotype throughout the natural mouse-tick-mouse cycle. The BBA66-deficient mutant isolate, Bb
ΔA66
, remained infectious in mice by needle inoculation of cultured organisms, but differences in spirochete burden and pathology in the tibiotarsal joint were observed relative to the parental wild-type (WT) strain.
Ixodes scapularis
larvae successfully acquired Bb
ΔA66
following feeding on infected mice, and the organisms persisted in these ticks through the molt to nymphs. A series of tick transmission experiments (
n
= 7) demonstrated that the ability of Bb
ΔA66
-infected nymphs to infect laboratory mice was significantly impaired compared to that of mice fed upon by WT-infected ticks.
trans
-complementation of Bb
ΔA66
with an intact copy of
bba66
restored the WT infectious phenotype in mice via tick transmission. These results suggest a role for BBA66 in facilitating
B. burgdorferi
dissemination and transmission from the tick vector to the mammalian host as part of the disease process for Lyme borreliosis.
Anaplasma phagocytophilum Inhibits Apoptosis and Promotes Cytoskeleton Rearrangement for Infection of Tick Cells
Authors: Ayllón Nieves , Villar Margarita , Busby Ann T. , Kocan Katherine M. , Blouin Edmour F. , Bonzón-Kulichenko Elena , Galindo Ruth C. , Mangold Atilio J. , Alberdi Pilar , Pérez de la Lastra José M. , Vázquez Jesús , de la Fuente José
Published: April 2013

Anaplasma phagocytophilum
causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects gene expression in both the vertebrate host and the tick vector,
Ixodes scapularis
. Here, we identified new genes, including spectrin alpha chain or alpha-fodrin (CG8) and voltage-dependent anion-selective channel or mitochondrial porin (T2), that are involved in
A. phagocytophilum
infection/multiplication and the tick cell response to infection. The pathogen downregulated the expression of CG8 in tick salivary glands and T2 in both the gut and salivary glands to inhibit apoptosis as a mechanism to subvert host cell defenses and increase infection. In the gut, the tick response to infection through CG8 upregulation was used by the pathogen to increase infection due to the cytoskeleton rearrangement that is required for pathogen infection. These results increase our understanding of the role of tick genes during
A. phagocytophilum
infection and multiplication and demonstrate that the pathogen uses similar strategies to establish infection in both vertebrate and invertebrate hosts.
Phylogeographic Origin of Helicobacter pylori Determines Host-Adaptive Responses upon Coculture with Gastric Epithelial Cells
Authors: Sheh Alexander , Chaturvedi Rupesh , Merrell D. Scott , Correa Pelayo , Wilson Keith T. , Fox James G.
Published: April 2013

While
Helicobacter pylori
infects over 50% of the world's population, the mechanisms involved in the development of gastric disease are not fully understood. Bacterial, host, and environmental factors play a role in disease outcome. To investigate the role of bacterial factors in
H. pylori
pathogenesis, global gene expression of six
H. pylori
isolates was analyzed during coculture with gastric epithelial cells. Clustering analysis of six Colombian clinical isolates from a region with low gastric cancer risk and a region with high gastric cancer risk segregated strains based on their phylogeographic origin. One hundred forty-six genes had increased expression in European strains, while 350 genes had increased expression in African strains. Differential expression was observed in genes associated with motility, pathogenicity, and other adaptations to the host environment. European strains had greater expression of the virulence factors
cagA
,
vacA
, and
babB
and were associated with increased gastric histologic lesions in patients. In AGS cells, European strains promoted significantly higher interleukin-8 (IL-8) expression than did African strains. African strains significantly induced apoptosis, whereas only one European strain significantly induced apoptosis. Our data suggest that gene expression profiles of clinical isolates can discriminate strains by phylogeographic origin and that these profiles are associated with changes in expression of the proinflammatory and protumorigenic cytokine IL-8 and levels of apoptosis in host epithelial cells. These findings support the hypothesis that bacterial factors determined by the phylogeographic origin of
H. pylori
strains may promote increased gastric disease.
Spinal epidural abscess treated with antibiotics alone
Authors: Pathak Ashish , Singh Poonam , Gehlot Prateek , Dhaneria Mamta
Published: April 2013

Spinal epidural abscess (SEA) is a rare clinical condition among children. Most patients do not present with classical signs. A 13-year-old boy without any predisposing factors presented with paraparesis, bladder and bowel involvement. MRI spine demonstrated an SEA at the C7 and D1 levels on both sides of the midline with cord oedema at the C2–3 to C6 level with minimal marrow oedema in the C6 vertebral body. We treated the patient with antibiotics (ceftriaxone and vancomycin) alone. The patient showed excellent response with only minimal residual gait disturbance at the end of 6 weeks of antibiotic therapy. This is the first paediatric report of complete recovery of a patient at clinical stage 4 following antibiotic treatment alone from India. However, caution should be exercised to closely monitor the patient’s recovery as any progression in the neurological state warrants surgery.
Obesity in young men, and individual and combined risks of type 2 diabetes, cardiovascular morbidity and death before 55 years of age: a Danish 33-year follow-up study
Authors: Schmidt Morten , Johannesdottir Sigrun A , Lemeshow Stanley , Lash Timothy L , Ulrichsen Sinna P , Bøtker Hans Erik , Toft Sørensen Henrik
Published: April 2013

Objectives

To examine the association between body mass index (BMI) in young adulthood and cardiovascular risks, including venous thromboembolism, before 55 years of age.

Design

Cohort study using population-based medical databases.

Setting

Outcomes registered from all hospitals in Denmark from 1977 onwards.

Participants

6502 men born in 1955 and eligible for conscription in Northern Denmark.

Main outcome measures

Follow-up began at participants’ 22nd birthday and continued until death, emigration or 55 years of age, whichever came first. Using regression analyses, we calculated the risks and HRs, adjusting for cognitive test score and years of education.

Results

48% of all obese young men (BMI ≥30 kg/m2) were either diagnosed with type 2 diabetes, hypertension, myocardial infarction, stroke or venous thromboembolism or died before reaching 55 years of age. Comparing obese men with normal weight men (BMI 18.5 to <25.0 kg/m2), the risk difference for any outcome was 28% (95% CI 19% to 38%) and the HR was 3.0 (95% CI 2.3 to 4.0). Compared with normal weight, obesity was associated with an event rate that was increased more than eightfold for type 2 diabetes, fourfold for venous thromboembolism and twofold for hypertension, myocardial infarction and death.

Conclusions

In this cohort of young men, obesity was strongly associated with adverse cardiometabolic events before 55 years of age, including venous thromboembolism. Compared with those of normal weight, young obese men had an absolute risk increase for type 2 diabetes, cardiovascular morbidity or premature death of almost 30%.
ELASTIC CURVES AND SURFACES UNDER LONG-RANGE FORCES: A GEOMETRIC APPROACH
Authors: SANTIAGO J. A. , CHACÓN-ACOSTA G. , GONZÁLEZ-GAXIOLA O.
Published: April 2013

Using classical differential geometry, the problem of elastic curves and surfaces in the presence of long-range interactions Φ, is posed. Starting from a variational principle, the balance of elastic forces and the corresponding projections ni⋅∇Φ, are found. In the case of elastic surfaces, a force coupling the mean curvature with the external potential, KΦ, appears; it is also present in the shape equation along the normal principal in the case of curves. The potential Φ contributes to the effective tension of curves and surfaces and also to the orbital torque. The confinement of a curve on a surface is also addressed, in such a case, the potential contributes to the normal force through the terms -κΦ-n⋅∇Φ. In general, the equation of motion becomes integro-differential that must be numerically solved.
ENERGY ESTIMATION FOR n-INPUT ADIABATIC LOGIC GATE: A PROPOSED ANALYTICAL MODEL
Authors: KANUNGO JITENDRA , DASGUPTA S.
Published: April 2013

In this paper, an analytical model is proposed to estimate the energy consumption of n-input adiabatic logic gate. The model is based on RC linearization of the adiabatic circuit network. To validate the model expressions, simulations are carried out at 90 nm technology node using the Cadence Spectre simulator. Model validates with simulation results at a maximum error equals to 9.94%. Model expressions are also applied in comparison of energy performance of adiabatic logic and conventional CMOS logic. Proposed research work suggests the operating conditions which makes the adiabatic logic more energy efficient than conventional CMOS logic.
GEOMETRIC NUMERICAL METHODS AND RESULTS IN THE CONTRAST IMAGING PROBLEM IN NUCLEAR MAGNETIC RESONANCE
Authors: BONNARD B. , COTS O.
Published: April 2013

The purpose of this paper is to present numerical methods and results about the contrast imaging problem in nuclear magnetic resonance which corresponds to a Mayer problem in optimal control. The candidates as minimizers are selected among a set of extremals, solutions of a Hamiltonian system given by the Pontryagin Maximum Principle and sufficient second order conditions are described. They form the geometric foundations of the HAMPATH code which combines shooting and continuation methods, see Ref. 9. The main contribution of this paper is to present a numerical analysis of the contrast imaging problem in NMR in the case of deoxygenated/oxygenated blood samples as an application of the aforementioned techniques.
HEAVY HADRON SPECTROSCOPY: A QUARK MODEL PERSPECTIVE
Authors: VIJANDE J. , VALCARCE A. , CARAMÉS T. F. , GARCILAZO H.
Published: April 2013

We present recent results of hadron spectroscopy and hadron–hadron interaction from the perspective of constituent quark models. We pay special attention to the role played by higher-order Fock space components in the hadron spectra and the connection of this extension with the hadron–hadron interaction. The main goal of our description is to obtain a coherent understanding of the low-energy hadron phenomenology without enforcing any particular model, to constrain its characteristics and learn about the low-energy realization of the theory.
MASS, MATTER, MATERIALIZATION, MATTERGENESIS AND CONSERVATION OF CHARGE
Authors: TSAN UNG CHAN
Published: April 2013

Conservation of mass in classical physics and in chemistry is considered to be equivalent to conservation of matter and is a necessary condition together with other universal conservation laws to account for observed experiments. Indeed matter conservation is associated to conservation of building blocks (molecules, atoms, nucleons, quarks and leptons). Matter is massive but mass and matter are two distinct concepts even if conservation of mass and conservation of matter represent the same reality in classical physics and chemistry. Conservation of mass is a consequence of conservation of atoms. Conservation of mass is valid because in these cases it is a very good approximation, the variation of mass being tiny and undetectable by weighing. However, nuclear physics and particle physics clearly show that conservation of mass is not valid to express conservation of matter. Mass is one form of energy, is a positive quantity and plays a fundamental role in dynamics allowing particles to be accelerated. Origin of mass may be linked to recently discovered Higgs bosons. Matter conservation means conservation of baryonic number A and leptonic number L, A and L being algebraic numbers. Positive A and L are associated to matter particles, negative A and L are associated to antimatter particles. All known interactions do conserve matter thus could not generate, from pure energy, a number of matter particles different from that of number of antimatter particles. But our universe is material and neutral, this double message has to be deciphered simultaneously. Asymmetry of our universe demands an interaction which violates matter conservation but obeys all universal conservation laws, in particular conservation of electric charge Q. Expression of Q shows that conservation of (A–L) and total flavor TF are necessary and sufficient to conserve Q. Conservation of A and L is indeed a trivial case of conservation of (A–L) and is valid for all known interactions of the standard model. Assumption of a novel interaction MC conserving (A–L) but violating simultaneously A and L (not trivial case of conservation) would allow energy to be transformed into a pair of baryon lepton or into a pair of antibaryon antilepton of opposite charges. This model could explain the asymmetric but nevertheless electrically neutral Universe but could not account for the numerical value of the tiny excess of matter over antimatter. The concept of anti-Universe would be superfluous. Observation of matter nonconservation processes would be of great interest to falsify this speculation.
STRUCTURAL ANALYSIS OF THE COMBUSTION SYNTHESIZED Y3+ DOPED CERIA (Ce0.9Y0.1O1.95)
Authors: JEYANTHI C. ESTHER , SIDDHESWARAN R. , KUMAR PUSHPENDRA , MANGALARAJA R. V. , SIVA SHANKAR V. , RAJARAJAN K.
Published: April 2013

Y 3+ doped CeO 2 nanopowders ( Ce 0.9 Y 0.1 O 1.95, abbreviated as YDC) were synthesized by citrate-nitrate-auto combustion process using cerium nitrate hexahydrate, yttrium nitrate hexahydrate and citric acid. The as-synthesized powders were calcined at 700°C and converted into dense bodies followed by sintering at 1200°C. The microstructure of the synthesized powders and sintered bodies were examined by scanning electron microscopy (SEM). The surface morphology of the nanoparticles and clusters were also analysed by transmission electron microscopy (TEM). The particles size of the YDC was found to be in the range from 10 to 30 nm, which is in good agreement with the crystallite size calculated from X-ray peak broadening method. Also, the X-ray diffraction confirmed that the Ce 0.9 Y 0.1 O 1.95 crystallizes as the cubic fluorite structure of pure ceria. The optical absorption by functional molecules, impurities and oxygen vacancies were analysed by FTIR and Raman spectroscopic studies. From the FTIR spectrum, the absorption peak found at 530 cm-1 is attributed to the vibrations of metal-oxygen bonds. The characteristic Raman peak was found to be 468 cm-1, and the minute absorption of oxygen vacancies were observed in the region 500–640 cm-1.
COUNTERPARTY RISK AND FUNDING: THE FOUR WINGS OF THE TVA
Authors: CRÉPEY STÉPHANE , GERBOUD RÉMI , GRBAC ZORANA , NGOR NATHALIE
Published: April 2013

The credit crisis and the ongoing European sovereign debt crisis have highlighted the native form of credit risk, namely the counterparty risk. The related credit valuation adjustment (CVA), debt valuation adjustment (DVA), liquidity valuation adjustment (LVA) and replacement cost (RC) issues, jointly referred to in this paper as total valuation adjustment (TVA), have been thoroughly investigated in the theoretical papers [8, 9]. The present work provides an executive summary and numerical companion to these papers, through which the TVA pricing problem can be reduced to Markovian pre-default TVA BSDEs. The first step consists in the counterparty clean valuation of a portfolio of contracts, which is the valuation in a hypothetical situation where the two parties would be risk-free and funded at a risk-free rate. In the second step, the TVA is obtained as the value of an option on the counterparty clean value process called contingent credit default swap (CCDS). Numerical results are presented for interest rate swaps in the Vasicek, as well as in the inverse Gaussian Hull-White short rate model, which allows also to assess the related model risk issue.
PRICING COUNTERPARTY RISK INCLUDING COLLATERALIZATION, NETTING RULES, RE-HYPOTHECATION AND WRONG-WAY RISK
Authors: BRIGO DAMIANO , CAPPONI AGOSTINO , PALLAVICINI ANDREA , PAPATHEODOROU VASILEIOS
Published: April 2013

This article is concerned with the arbitrage-free valuation of bilateral counterparty risk through stochastic dynamical models when collateral is included, with possible rehypothecation. The payout of claims is modified to account for collateral margining in agreement with International Swap and Derivatives Association (ISDA) documentation. The analysis is specialized to interest-rate and credit derivatives. In particular, credit default swaps are considered to show that a perfect collateralization cannot be achieved under default correlation. Interest rate and credit spread volatilities are fully accounted for, as is the impact of re-hypothecation, collateral margining frequency, and dependencies.
ON VALUATION WITH STOCHASTIC PROPORTIONAL HAZARD MODELS IN FINANCE
Authors: YAMAZAKI AKIRA
Published: April 2013

While the proportional hazard model is recognized to be statistically meaningful for analyzing and estimating financial event risks, the existing literature that analytically deals with the valuation problems is very limited. In this paper, adopting the proportional hazard model in continuous time setting, we provide an analytical treatment for the valuation problems. The derived formulas, which are based on the generalized Edgeworth expansion and give approximate solutions to the valuation problems, are widely useful for evaluating a variety of financial products such as corporate bonds, credit derivatives, mortgage-backed securities, saving accounts and time deposits. Furthermore, the formulas are applicable to the proportional hazard model having not only continuous processes (e.g., Gaussian, affine, and quadratic Gaussian processes) but also discontinuous processes (e.g., Lévy and time-changed Lévy processes) as stochastic covariates. Through numerical examples, it is demonstrated that very accurate values can be quickly obtained by the formulas such as a closed-form formula.
CLIFFORD SPACE GRAVITATIONAL FIELD EQUATIONS AND DARK ENERGY
Authors: CASTRO CARLOS
Published: April 2013

We continue with the study of Clifford-space (C-space) gravity and analyze further the C-space generalized gravitational field equations which are obtained from a variational principle based on the generalization of the Einstein–Hilbert–Cartan action. One of the main features is that the C-space connection requires torsion in order to have consistency with the Clifford algebraic structure associated with the curved C-space basis generators. Hence no spin matter is required to induce torsion since it already exists in the vacuum. The field equations in C-spaces associated to a Clifford algebra in D dimensions are not equivalent to the ordinary gravitational equations with torsion in higher 2D dimensions. The most physically relevant conclusion, besides the presence of torsion in the vacuum, is the contribution of the higher grade metric components gμ1μ2ν1ν2, gμ1μ2μ3ν1ν2ν3,… of the C-space metric to dark energy/dark matter.
Human-centered computing
Authors: Guzdial Mark
Published: April 2013

Combining computing and psychology, J.C.R. Licklider's prescient ideas are being applied in contemporary educational settings.
Batch Effects and Pathway Analysis: Two Potential Perils in Cancer Studies Involving DNA Methylation Array Analysis
Authors: Harper Kristin N. , Peters Brandilyn A. , Gamble Mary V.
Published: April 2013

Background: DNA methylation microarrays have become an increasingly popular means of studying the role of epigenetics in cancer, although the methods used to analyze these arrays are still being developed and existing methods are not always widely disseminated among microarray users.

Methods: We investigated two problems likely to confront DNA methylation microarray users: (i) batch effects and (ii) the use of widely available pathway analysis software to analyze results. First, DNA taken from individuals exposed to low and high levels of drinking water arsenic were plated twice on Illumina's Infinium 450 K HumanMethylation Array, once in order of exposure and again following randomization. Second, we conducted simulations in which random CpG sites were drawn from the 450 K array and subjected to pathway analysis using Ingenuity's IPA software.

Results: The majority of differentially methylated CpG sites identified in Run One were due to batch effects; few sites were also identified in Run Two. In addition, the pathway analysis software reported many significant associations between our data, randomly drawn from the 450 K array, and various diseases and biological functions.

Conclusions: These analyses illustrate the pitfalls of not properly controlling for chip-specific batch effects as well as using pathway analysis software created for gene expression arrays to analyze DNA methylation array data.

Impact: We present evidence that (i) chip-specific effects can simulate plausible differential methylation results and (ii) popular pathway analysis software developed for expression arrays can yield spurious results when used in tandem with methylation microarrays. Cancer Epidemiol Biomarkers Prev; 22(6); 1052–60. ©2013 AACR.
Chromosomal Instability, DNA Index, Dysplasia, and Subsite in Oral Premalignancy as Intermediate Endpoints of Risk of Cancer
Authors: Giaretti Walter , Monteghirfo Stefano , Pentenero Monica , Gandolfo Sergio , Malacarne Davide , Castagnola Patrizio
Published: April 2013

Background: Chromosomal instability and aneuploidy may represent biomarkers of oral exposure to damaging agents and early signs of clinical disease according to the theory of “oral field cancerization.”

Methods: The hypothesis was tested that the DNA index (DI) values, obtained by high-resolution DNA flow cytometry (DNA-FCM), may potentially contribute to oral cancer risk prediction. For this purpose, the DI of oral fields of normal-appearing mucosa and oral potentially malignant disorders (OPMDs) in 165 consecutive patients was tested for association with dysplasia and/or the oral subsites of tongue and floor of the mouth taken as high-risk intermediate endpoints surrogate of cancer clinical endpoints. The association was evaluated by logistic regression using patient gender, age, tobacco, cigarette smoking habit, and alcohol abuse as confounding variables.

Results: Different DI models provided evidence of statistical significant associations. Subdividing the DI values in diploid, near-diploid aneuploid, and high or multiple aneuploid from both OPMDs and oral normal-appearing mucosa, ORs, respectively, of 1, 4.3 (P = 0.001), and 18.4 (P < 0.0005) were obtained.

Conclusion: Routine DI analysis by high-resolution DNA-FCM seems potentially useful to complement dysplasia and subsite analysis for assessment of oral cancer risk prediction and for a better management of the patients with OPMDs. Work is in progress to validate the present findings in a prospective study with clinical endpoints.

Impact: Identifying DNA abnormalities in oral premalignancy may lead to biomarkers of oral exposure and cancer risk and potentially to more effective prevention measures. Cancer Epidemiol Biomarkers Prev; 22(6); 1133–41. ©2013 AACR.
Prolonged Inhibition of Glioblastoma Xenograft Initiation and Clonogenic Growth following In Vivo Notch Blockade
Authors: Chu Qian , Orr Brent A. , Semenkow Samantha , Bar Eli E. , Eberhart Charles G.
Published: April 2013

Purpose: To examine the effects of clinically relevant pharmacologic Notch inhibition on glioblastoma xenografts.

Experimental Design: Murine orthotopic xenografts generated from temozolomide-sensitive and -resistant glioblastoma neurosphere lines were treated with the γ-secretase inhibitor MRK003. Tumor growth was tracked by weekly imaging, and the effects on animal survival and tumor proliferation were assessed, along with the expression of Notch targets, stem cell, and differentiation markers, and the biology of neurospheres isolated from previously treated xenografts and controls.

Results: Weekly MRK003 therapy resulted in significant reductions in growth as measured by imaging, as well as prolongation of survival. Microscopic examination confirmed a statistically significant reduction in cross-sectional tumor area and mitotic index in a MRK003-treated cohort as compared with controls. Expression of multiple Notch targets was reduced in the xenografts, along with neural stem/progenitor cell markers, whereas glial differentiation was induced. Neurospheres derived from MRK003-treated xenografts exhibited reduced clonogenicity and formed less aggressive secondary xenografts. Neurospheres isolated from treated xenografts remained sensitive to MRK003, suggesting that therapeutic resistance does not rapidly arise during in vivo Notch blockade.

Conclusions: Weekly oral delivery of MRK003 results in significant in vivo inhibition of Notch pathway activity, tumor growth, stem cell marker expression, and clonogenicity, providing preclinical support for the use of such compounds in patients with malignant brain tumors. Some of these effects can persist for some time after in vivo therapy is complete. Clin Cancer Res; 19(12); 3224–33. ©2013 AACR.
Reference Ranges of Ductus Arteriosus Derived by Cardio-Spatiotemporal Image Correlation from 14 to 40 Weeks of Gestation
Authors: Traisrisilp Kuntharee , Tongprasert Fuanglada , Srisupundit Kasemsri , Luewan Suchaya , Tongsong Theera
Published: April 2013

Objective: To construct reference ranges of fetal ductus arteriosus (DA) derived by volume datasets of cardio-spatiotemporal image correlation (cardio-STIC). Methods: Cardio-STIC volume datasets were acquired from low-risk singleton pregnancies with a reliable gestational age from 14 to 40 weeks. In offline analysis with 4D View version 9, fetal DA was measured in the transverse ductal arch view with orthogonal control in the multiplanar view. The reference ranges of the DA and Z-score equation were constructed against gestational weeks and biparietal diameter (BPD) as independent variables. Results: A total of satisfactory 606 volumes were analyzed. The reference ranges for predicting means and SDs of fetal DA were constructed based on the best-fit regression model. Mean DA (mm) was best predicted by linear model as a function of GA (weeks) and BPD (cm) as follows: Predicted DA diameter (cm) = -0.051 + 0.014 × GA (weeks) (r = 0.84) and Predicted DA diameter (cm) = -0.015 + 0.053 × BPD (cm) (r = 0.83). Models for Z-score calculation and centile charts for predicting fetal DA were also provided. Conclusion: Reference ranges of the fetal DA and Z-score model are provided. These may serve as a useful tool in the assessment of fetal DA, especially in fetal cardiac anomalies or in monitoring fetuses exposed to maternal indomethacin.
Angiotensin II Promotes Thoracic Aortic Dissections and Ruptures in
Col3a1
Haploinsufficient Mice
Authors: Faugeroux Julie , Nematalla Hany , Li Weiwei , Clement Marc , Robidel Estelle , Frank Michael , Curis Emmanuel , Ait-Oufella Hafid , Caligiuri Giuseppina , Nicoletti Antonino , Hagege Albert , Messas Emmanuel , Bruneval Patrick , Jeunemaitre Xavier , Bergaya Sonia
Published: April 2013

Vascular Ehlers–Danlos syndrome is a dramatic inherited disease caused by mutations of type III collagen (
COL3A1
) gene, associated with early-onset occurrence of arterial ruptures.
Col3a1
+/−
heterozygous mice, the only vascular Ehlers–Danlos syndrome model available to date, have no spontaneous early vascular phenotype. Our objective was to determine the susceptibility of
Col3a1
+/−
mice to develop arterial ruptures under high blood pressure (BP) conditions induced by a 4-week infusion of angiotensin II (AngII). AngII (1 μg/kg per minute) significantly and comparably increased systolic BP in
Col3a1
+/−
and
Col3a1
+/+
mice but led to a higher premature mortality rate in
Col3a1
+/−
mice compared with
Col3a1
+/+
mice (73% versus 36%;
P
=0.03), particularly during the first-week infusion (55% versus 0%). Echocardiography and histological analysis evidenced that early deaths were caused by thoracic aortic ruptures preceded by dissections and associated with low aortic collagen fibrils content. Remarkably, lowering the dose of AngII (0.5 μg/kg per minute) rescued the first-week premature deaths of
Col3a1
+/−
mice while decreasing the rises in systolic BP (
P
=0.05 compared with the high-dose AngII), resulting in similar mortality rates in both groups of mice at the end of the 4-week period (30% versus 50% in
Col3a1
+/−
and
Col3a1
+/+
mice;
P
=0.30). Finally, norepinephrine infusion (3.9 μg/kg per minute) did not induced significant mortality in both groups, whereas it significantly increased systolic BP, comparably with the high and with the low dose of AngII in
Col3a1
+/−
mice (
P
=0.53 and
P
=1.00, respectively). Our findings demonstrated the extreme sensitivity of
Col3a1
insufficient mice to prematurely develop thoracic aortic ruptures in response to AngII and its associated high levels in BP.