bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on a Pulsating Heat Pipe With Self-Rewetting Fluid
Authors: Fumoto Koji , Kawaji Masahiro , Kawanami Tsuyoshi
Published: September 2010

This paper discusses a pulsating heat pipe (PHP) using a self-rewetting fluid. Unlike other common liquids, self-rewetting fluids have the property that the surface tension increases with temperature. The increasing surface tension at a higher temperature can cause the liquid to be drawn toward a heated surface if a dry spot appears and thus to improve boiling heat transfer. In experiments, 1-butanol and 1-pentanol were added to water at a concentration of less than 1 wt % to make self-rewetting fluid. A pulsating heat pipe made from an extruded multiport tube was partially filled with the self-rewetting fluid water mixture and tested for its heat transport capability at different input power levels. The experiments showed that the maximum heat transport capability was enhanced by a factor of 4 when the maximum heater temperature was limited to 110°C. Thus, the use of a self-rewetting fluid in a PHP was shown to be highly effective in improving the heat transport capability of pulsating heat pipes.
Coordinated Optimization of Cooling and IT Power in Data Centers
Authors: Samadiani Emad , Amur Hrishikesh , Krishnan Bhavani , Joshi Yogendra , Schwan Karsten
Published: September 2010

Concurrency and exchanging design knowledge among thermal and IT management are required to achieve an energy efficient operational data center. In this paper, a design approach is presented to bring adaptability and concurrency for coordinated minimization of cooling and IT power consumption in data centers. The presented approach is centered on a proper orthogonal decomposition based reduced order thermal modeling approach, and power profiling of the IT equipment to identify the optimal parameters of the air cooling systems along with optimal dynamic workload distribution among the servers. The method is applied to a data center cell with different rack and server architectures. The results show that the design approach results in 12–70% saving in the total energy consumption of the data center cell for various scenarios, compared with a baseline design.
Silver Flip-Chip Technology by Solid-State Bonding
Authors: Wang Pin J. , Lee Chin C.
Published: September 2010

Silver flip-chip joints between silicon (Si) chips and copper (Cu) substrates were fabricated using a solid-state bonding process without any solder and without flux. The bonding process was performed at 250°C, compatible with typical reflow temperature for lead-free solders. During the bonding process, there was no molten phase involved. The Ag joints fabricated consisted of only pure Ag without any intermetallic compound (IMC). Thus, reliability issues associated with IMCs and IMC growth do not exist anymore. Silver has the highest electrical conductivity and highest thermal conductivity among all metals. It is also quite ductile and able to deform to release stresses caused by thermal expansion mismatch. Flip-chip joints of high aspect ratio can be accomplished because the joints stay in a solid state during the bonding process. It looks like that silver is the ultimate joining material for flip-chip as well as through-Si-via interconnect technologies. In this study, the solid-state bonding process was first developed using a pure Ag foil to bond a Si chip to a Cu substrate in one step. The bonding strength on two interfaces, Si/Ag and Ag/Cu, passes the MIL-STD-883G Method 2019.7. To demonstrate Ag flip-chip interconnects, Si chips were electroplated with Ag bumps, followed by the solid-state bonding process on Cu substrates. The flip-chip bumps are well bonded to the Cu substrate. It would take some time for this new technology to be probably accepted and utilized in production. On the other hand, the preliminary results in this study show that Ag flip-chip joints can indeed be fabricated at 250°C.
Phosphor Concentration Effects on Optothermal Characteristics of Phosphor Converted White Light-Emitting Diodes
Authors: You Jiun Pyng , Lin Yeong-Her , Tran Nguyen T. , Shi Frank G.
Published: September 2010

The thermal and optical characteristics of phosphor converted white light-emitting diodes (LEDs) with different phosphor concentrations ranging from 4 wt % to 13 wt % are investigated. The light output of LEDs with higher phosphor concentration is found to have larger degradation in constant current compared with pulse current than that with lower phosphor concentration. In addition, the junction temperatures of phosphor converted white LEDs raise with increasing phosphor concentration, so that the decreased phosphor conversion efficiency is observed both in pulse and constant current modes. The physical mechanisms for these observations are discussed. This study elucidates the phosphor dependent optical and thermal behavior of phosphor converted white LEDs.
Modeling Bioheat Transport at Macroscale
Authors: Wang Liqiu , Fan Jing
Published: September 2010

Macroscale thermal models have been developed for biological tissues either by the mixture theory of continuum mechanics or by the porous-media theory. The former uses scaling-down from the global scale; the latter applies scaling-up from the microscale by the volume averaging. The used constitutive relations for heat flux density vector include the Fourier law, the Cattaneo–Vernotte (Cattaneo, C., 1958, “A Form of Heat Conduction Equation Which Eliminates the Paradox of Instantaneous Propagation,” Compt. Rend., 247, pp. 431–433; Vernotte, P., 1958, “Les Paradoxes de la Théorie Continue de I’equation de la Chaleur,” Compt. Rend., 246, pp. 3154–3155) theory, and the dual-phase-lagging theory. The developed models contain, for example, the Pennes (1948, “Analysis of Tissue and Arterial Blood Temperature in the Resting Human Forearm,” J. Appl. Physiol., 1, pp. 93–122), Wulff (1974, “The Energy Conservation Equation for Living Tissues,” IEEE Trans. Biomed. Eng., BME-21, pp. 494–495), Klinger (1974, “Heat Transfer in Perfused Tissue I: General Theory,” Bull. Math. Biol., 36, pp. 403–415), and Chen and Holmes (1980, “Microvascular Contributions in Tissue Heat Transfer,” Ann. N.Y. Acad. Sci., 335, pp. 137–150), thermal wave bioheat, dual-phase-lagging (DPL) bioheat, two-energy-equations, blood DPL bioheat, and tissue DPL bioheat models. We analyze the methodologies involved in these two approaches, the used constitutive theories for heat flux density vector and the developed models. The analysis shows the simplicity of the mixture theory approach and the powerful capacity of the porous-media approach for effectively developing accurate macroscale thermal models for biological tissues. Future research is in great demand to materialize the promising potential of the porous-media approach by developing a rigorous closure theory. The heterogeneous and nonisotropic nature of biological tissue yields normally a strong noninstantaneous response between heat flux and temperature gradient in nonequilibrium heat transport. Both blood and tissue macroscale temperatures satisfy the DPL-type energy equations with the same values of the phase lags of heat flux and temperature gradient that can be computed in terms of blood and tissue properties, blood-tissue interfacial convective heat transfer coefficient, and blood perfusion rate. The blood-tissue interaction leads to very sophisticated effect of the interfacial convective heat transfer, the blood velocity, the perfusion, and the metabolic reaction on blood and tissue macroscale temperature fields such as the spreading of tissue metabolic heating effect into the blood DPL bioheat equation and the appearance of the convection term in the tissue DPL bioheat equation due to the blood velocity.
Skin Electroporation With Passive Transdermal Transport Theory: A Review and a Suggestion for Future Numerical Model Development
Authors: Becker S. M.
Published: September 2010

Skin electroporation is an approach used to enhance the transdermal transport of large molecules in which the skin is exposed to a series of electric pulses, resulting in the structural alteration of the stratum corneum. This article suggests the use of passive transdermal transport models in combination with models depicting the electrically induced structural alterations in order to advance the modeling development of transport associated with skin electroporation. A review of the major physical phenomena observed in skin electroporation transport experiments is provided. A compendium of representative models is made available through a review of the current understanding of the two fields: (1) porous media descriptions of nondestructive transdermal transport and (2) modeling electroporation related structural changes within the skin. To show the applicability and potential of merging transdermal transport modeling with skin electroporation modeling, an example model is developed that combines a brick and mortar style skin representation with a thermodynamic based model of skin electroporation.
Modeling of Fibroblast-Controlled Strengthening and Remodeling of Uniaxially Constrained Collagen Gels
Authors: Kroon Martin
Published: September 2010

A theoretical model for the remodeling of collagen gels is proposed. The collagen fabric is modeled as a network of collagen fibers, which in turn are composed of collagen fibrils. In the model, the strengthening of collagen fabric is accomplished by fibroblasts, which continuously recruit and attach more collagen fibrils to existing collagen fibers. The fibroblasts also accomplish a reorientation of collagen fibers. Fibroblasts are assumed to reorient collagen fibers toward the direction of maximum material stiffness. The proposed model is applied to experiments in which fibroblasts were inserted into a collagen gel. The model is able to predict the force-strain curves for the experimental collagen gels, and the final distribution of collagen fibers also agrees qualitatively with the experiments.
High Frequency of Horizontal Gene Transfer in the Oceans
Authors: McDaniel Lauren D. , Young Elizabeth , Delaney Jennifer , Ruhnau Fabian , Ritchie Kim B. , Paul John H.
Published: September 2010

Viruslike particles enable lateral gene transfer among marine microorganisms.
Allosteric Supramolecular Triple-Layer Catalysts
Authors: Yoon Hyo Jae , Kuwabara Junpei , Kim Jun-Hyun , Mirkin Chad A.
Published: September 2010

Chloride Control of a Catalyst

Allosteric regulation of proteins and enzymes allows their conformation to be controlled by changes in the concentration of effector-binding molecules; reactivity can be controlled by changing access to the active catalytic site. The supramolecular control of conformation through multiple weaker interactions has been exploited in organometallic catalysts that can open or close access to reactive sites around a metal center.

Yoon
et al.

(p.
66
) now show how chloride ions can be used to control a rhodium polymerization catalyst in which two metal centers are bridged by a linker bearing aromatic groups. When Cl
−
is present, reactive sites remain available on the metal centers. When Cl
−
is removed by abstracting agents, aromatic groups on one of the other ligands on the Rh centers can bind to the linker to form a triple-layer sandwich structure. Formation of this supramolecular structure blocks access of reactants to the metal centers.
A Balancing Act for Taxol Precursor Pathways in
E. coli
Authors: Liu Tiangang , Khosla Chaitan
Published: September 2010

A fermentation process that balances the activities of several bacterial and plant enzymes makes a precursor to an anticancer drug in substantial quantities.
Complex Systems View of Educational Policy Research
Authors: Maroulis S. , Guimerà R. , Petry H. , Stringer M. J. , Gomez L. M. , Amaral L. A. N. , Wilensky U.
Published: September 2010

Agent-based modeling and network analysis can help integrate knowledge on “micro-level” mechanisms and “macro-level” effects.
Mosaicism—Switch or Spectrum?
Authors: Davis Brian R. , Candotti Fabio
Published: September 2010

A high rate of recombination restores the function of a mutated gene that encodes keratin, giving rise to the “confetti” spots in a rare skin disorder.
The Future of Russian Science
Authors: Georgiev Georgii , Sverdlov Eugene
Published: September 2010

In May, Russian Prime Minister Vladimir Putin addressed the general meeting of the Russian Academy of Sciences (RAS), describing plans to overhaul the country's science and innovation agenda and structure, with the goal of bolstering Russia's economy and global competitiveness. A major question is what role the RAS—the largest and most prestigious scientific institution in Russia—will have in these projects.
Academy Rankings Tell You a Lot, But Not Who's No. 1 in Any Field
Authors: Mervis Jeffrey
Published: September 2010

This week's release of the long-awaited assessment of the quality of U.S. research doctoral programs by the National Academies' National Research Council will disappoint those who simply want to know who's No. 1 in any particular field, because the NRC assessment can look quite different depending on your definition of "best."
India's Vision: From Scientific Pipsqueak to Powerhouse
Authors: Bagla Pallava
Published: September 2010

A new report offers a stinging indictment of India's scientific frailties, noting that science here is "severely hampered by oppressive bureaucratic practices and inflexible administrative and financial controls."
Filling Gaps in Global Biodiversity Estimates
Authors: Pennisi Elizabeth
Published: September 2010

Earlier this week, researchers helped fill gaps in the data on the conservation status of species by using an innovative statistical approach called the Sampled Red List Index. The new index is a response to growing frustrations with the International Union for Conservation of Nature's Red List of Threatened Species, which is an ongoing tally of which species are known to be in trouble.
Archaeologists See Big Promise In Going Molecular
Authors: Travis John
Published: September 2010

Creative applications for ancient DNA emerged at a meeting, where researchers also described studies of other preserved molecules, including ancient RNA and proteins.
Killer Bots Are Getting Human
Authors: Bohannon John
Published: September 2010

The bot that won the third annual 2K BotPrize, a competition to create artificially intelligent game-playing agents that can fool a judge into believing they are human, represents a leap forward for game AI because the team used machine consciousness rather than just mimicking human behaviors.
Smarts for Serious Games
Authors: Bohannon John
Published: September 2010

Games used for teaching or training face big problems because of their simple programming. A computer scientist presented a solution to those problems at the meeting: a new architecture for so-called serious games that uses artificial-intelligence techniques similar to those in some of the latest video games.
Reducing Blood Culture Contamination by a Simple Informational Intervention
Authors: Roth A. , Wiklund A. E. , Pålsson A. S. , Melander E. Z. , Wullt M. , Cronqvist J. , Walder M. , Sturegård E.
Published: September 2010

Compared to truly negative cultures, false-positive blood cultures not only increase laboratory work but also prolong lengths of patient stay and use of broad-spectrum antibiotics, both of which are likely to increase antibiotic resistance and patient morbidity. The increased patient suffering and surplus costs caused by blood culture contamination motivate substantial measures to decrease the rate of contamination, including the use of dedicated phlebotomy teams. The present study evaluated the effect of a simple informational intervention aimed at reducing blood culture contamination at Skåne University Hospital (SUS), Malmö, Sweden, during 3.5 months, focusing on departments collecting many blood cultures. The main examined outcomes of the study were pre- and postintervention contamination rates, analyzed with a multivariate logistic regression model adjusting for relevant determinants of contamination. A total of 51,264 blood culture sets were drawn from 14,826 patients during the study period (January 2006 to December 2009). The blood culture contamination rate preintervention was 2.59% and decreased to 2.23% postintervention (odds ratio, 0.86; 95% confidence interval, 0.76 to 0.98). A similar decrease in relevant bacterial isolates was not found postintervention. Contamination rates at three auxiliary hospitals did not decrease during the same period. The effect of the intervention on phlebotomists' knowledge of blood culture routines was also evaluated, with a clear increase in level of knowledge among interviewed phlebotomists postintervention. The present study shows that a relatively simple informational intervention can have significant effects on the level of contaminated blood cultures, even in a setting with low rates of contamination where nurses and auxiliary nurses conduct phlebotomies.
Aggregatibacter actinomycetemcomitans
as an Early Colonizer of Oral Tissues: Epithelium as a Reservoir?
Authors: Fine Daniel H. , Markowitz Kenneth , Furgang David , Velliyagounder Kabilan
Published: September 2010

This study examined
in vivo
and
in vitro
colonization by
Aggregatibacter actinomycetemcomitans
, an organism highly associated with aggressive periodontitis. Thirteen volunteers (5 were
A. actinomycetemcomitans
positive for buccal epithelial cells [BECs] and teeth, 5 were
A. actinomycetemcomitans
positive for teeth only, and 3 were
A. actinomycetemcomitans
-negative controls) had two mandibular stents fabricated. Each stent contained 3 removable hydroxyapatite (HA) tooth surrogates. One HA square was removed from a stent at 5 time points over 7 h to assess the transfer of
A. actinomycetemcomitans
from teeth or BECs to HA.
Streptococcus
,
Actinomyces
,
A. actinomycetemcomitans
, and total anaerobic counts were evaluated on each square over time.
In vitro
experiments evaluated binding, desorption, transfer, and reattachment of
A. actinomycetemcomitans
wild-type and mutant strains to BECs and saliva-coated HA (SHA).
Streptococcus
and
Actinomyces
formed 80% of the cultivable flora on HA in all subjects. Transfer of
A. actinomycetemcomitans
to HA was not seen in subjects with
A. actinomycetemcomitans
on teeth only. All 5 subjects with
A. actinomycetemcomitans
on BECs showed transfer of
A. actinomycetemcomitans
to HA.
In vitro
,
A. actinomycetemcomitans
desorbed from BECs and transferred to SHA.
A. actinomycetemcomitans
binding to SHA was irreversible and did not transfer to BECs. The adhesin Aae showed specificity for BECs. Fimbrial mutants showed the greatest reduction in binding to SHA.
A. actinomycetemcomitans
migrated from BECs to HA
in vivo
and to SHA
in vitro
; however,
A. actinomycetemcomitans
movement from teeth and SHA to BECs did not occur.
In vivo
,
A. actinomycetemcomitans
colonized HA within 6 h and thus can be considered an early colonizer. BECs are a likely reservoir for
A. actinomycetemcomitans
tooth colonization.
Evaluation of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Analysis and Spoligotyping for Genotyping of
Mycobacterium bovis
Isolates and a Comparison with Restriction Fragment Length Polymorphism Typing
Authors: McLernon Joanne , Costello Eamon , Flynn Orla , Madigan Gillian , Ryan Fergus
Published: September 2010

Common strain typing methods for differentiation of
Mycobacterium bovis
isolates include restriction endonuclease analysis (REA), restriction fragment length polymorphism (RFLP) analysis, spoligotyping, and, more recently, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. MIRU-VNTR typing and spoligotyping were evaluated in this study, and these typing methods were compared with RFLP typing. A total of 386
M. bovis
isolates from cattle, badgers, and deer in the Republic of Ireland that had previously been typed by IS
6110
, polymorphic GC-rich sequence (PGRS), and direct-repeat (DR) RFLP were included in the study. Spoligotyping and analysis of six VNTR loci (QUB 11a, QUB 11b, ETR A, 4052, MIRU 26, and 1895) were performed on the samples. RFLP analysis was the method that gave the greatest differentiation of strains, with a Hunter-Gaston discriminatory index (HGDI) of 0.927; the HGDI recorded for MIRU-VNTR typing was marginally lower at 0.918, and spoligotyping was the least discriminatory method, with an HGDI of 0.7. Spoligotype SB0140 represented approximately 50% of the isolates. Within the group of isolates represented by SB0140, there was a much lower level of concordance between RFLP and MIRU-VNTR typing than for groups represented by other spoligotypes. A combination of spoligotyping and MIRU-VNTR typing offered advantages over MIRU-VNTR typing alone. In a combined spoligotyping and MIRU-VNTR typing protocol, the number of VNTR loci could be reduced to four (QUB 11a, QUB 11b, ETR A, and 4052) while maintaining a high level of strain differentiation.
Bacteremia Caused by a Novel
Helicobacter
Species in a 28-Year-Old Man with X-Linked Agammaglobulinemia
Authors: Schwarze-Zander Carolynne , Becker Sabine , Wenzel Jörg , Rockstroh Jürgen K. , Spengler Ulrich , Yassin Atteyet F.
Published: September 2010

We report on a case of bacteremia caused by a previously unknown urease-negative
Helicobacter
strain, IMMIB HP-28/08, isolated from blood cultures of a 28-year-old man with X-linked agammaglobulinemia. The identification of the isolate was based on 16S rRNA gene sequencing. In the phylogenetic tree, the isolate fell into a cluster which included
Helicobacter canadensis
,
Helicobacter equorum
, and
Helicobacter pullorum
. This is the first report of bacteremia caused by this fastidious organism. Further investigations are necessary to determine the potential role of this species as a pathogen of bloodstream infections.
Hepatitis B Virus (HBV) Subgenotypes C2 and B2 Differ in Lamivudine- and Adefovir-Resistance-Associated Mutational Patterns in HBV-Infected Chinese Patients
Authors: Li Xiaodong , Wang Lin , Zhong Yanwei , Wong Vincent Wai-Sun , Xu Zhihui , Liu Yan , Li Qinghong , Xin Shaojie , Zhao Jingmin , Xu Dongping
Published: September 2010

We aimed to study the prevalence and clinical implications of hepatitis B virus (HBV) subgenotypes in Chinese patients. A total of 4,300 patients, mainly from northern China, were enrolled, including 182 patients with acute hepatitis B and 4,118 patients with chronic HBV infection who had been exposed to nucleoside or nucleotide analogs. HBV genotypes/subgenotypes were determined by direct sequencing of the HBV S/Pol region. The prevalence rates were 0.40% for HBV/B1, 14.30% for HBV/B2, 0.25% for HBV/B3, 0.35% for HBV/B4, 1.05% for HBV/C1, 81.72% for HBV/C2, 0.93% for HBV/C3, 0.16% for HBV/C4, and 0.84% for HBV/D. In chronic HBV infection, patients with HBV/B2 were younger and had lower ΗBeAg positive rates than patients with HBV/C2. The incidence of lamivudine-resistant mutations was significantly higher in HBV/C2 compared to HBV/B2 (27.9% versus 19.8%;
P
< 0.01), and the significant difference was observed only for rtM204I and not rtM204V. In addition, compensatory mutations were more frequently detected in HBV/C2. The incidence of adefovir-resistant mutations was similar between the two subsets, but HBV/C2 inclined to show rtA181V (3.6% for C2 versus 0.9% for B2;
P
< 0.01), while HBV/B2 inclined to show rtN236T (4.5% for versus 2.5% for C2;
P
< 0.01). The ratios of HBV/B2 to HBV/C2 infection were 1.7 (110/65), 5.7 (2,653/463), 7.5 (520/69), 8.0 (48/6), and 15.3 (183/12) for acute hepatitis B, chronic hepatitis B, liver cirrhosis, acute-on-chronic liver failure, and hepatocellular carcinoma, respectively. In conclusion, HBV
/
C2 and HBV/B2, two prevalent subgenotypes, differ in lamivudine- and adefovir-resistance-associated mutational patterns. HBV/C2-infected patients are more likely to have disease progression than HBV/B2-infected ones.
Evaluation of Updated Interpretative Criteria for Categorizing
Klebsiella pneumoniae
with Reduced Carbapenem Susceptibility
Authors: Endimiani Andrea , Perez Federico , Bajaksouzian Saralee , Windau Anne R. , Good Caryn E. , Choudhary Yuvraj , Hujer Andrea M. , Bethel Christopher R. , Bonomo Robert A. , Jacobs Michael R.
Published: September 2010

We studied the accuracy of various susceptibility testing methods, including the 2009, 2010, and updated 2010 CLSI recommendations, to identify
Klebsiella pneumoniae
isolates with reduced susceptibility to carbapenems associated with different mechanisms of resistance. Forty-three wild-type (WT) strains, 42 extended-spectrum β-lactamase (ESBL) producers, 18 ESBL producers with outer membrane porin protein loss (ESBL/Omp strains), and 42
bla
KPC
-possessing
K. pneumoniae
(KPC-Kp) isolates were evaluated. Imipenem (IPM), meropenem (MEM), ertapenem (ERT), and doripenem (DOR) were tested by broth microdilution (BMD), Etest, and disk diffusion (DD), and the modified Hodge test (MHT) was performed using IPM and MEM disks. Results were interpreted according to original as well as recently updated interpretative criteria. MHT was positive for all 42 KPC-Kp isolates and 10 of 18 ESBL/Omp strains and therefore had poor specificity in differentiating between KPC-Kp and ESBL/Omp isolates. Based on the updated CLSI standards, phenotypic susceptibility testing by BMD and DD differentiated most carbapenem-susceptible from carbapenem-nonsusceptible
K. pneumoniae
isolates without the need for MHT, while the Etest method characterized many KPC-Kp isolates as susceptible, and breakpoints may need to be lowered for this method. However, both the original and updated CLSI criteria do not adequately differentiate between isolates in the KPC-Kp group, which are unlikely to respond to carbapenem therapy, and those in the ESBL/Omp group, which are likely to respond to carbapenem therapy if MICs are within pharmacokinetic/pharmacodynamic targets. Further studies are required to determine if there is a clinical need to differentiate between KPC-Kp and ESBL/Omp groups.
Peptide Inhibitors of Flavivirus Entry Derived from the E Protein Stem
Authors: Schmidt Aaron G. , Yang Priscilla L. , Harrison Stephen C.
Published: September 2010

Peptides derived from the “stem” of dengue virus (DV) type 2 (DV2) envelope (E) protein inhibit DV2 infectivity, targeting a late-stage fusion intermediate. We show here that stem peptides from all DV serotypes cross-inhibit DV1 to DV4 but that corresponding peptides derived from related flaviviruses do not. This failure to inhibit infection is not due to poor interaction with the E protein but rather to loss of association with the virion membrane. Residues 442 to 444 of the stem are determinants of inhibition; increasing hydrophobicity in this region increases inhibitory strength. These results support a two-step model of how stem-derived peptides inhibit viral entry.
Structure of a Major Antigenic Site on the Respiratory Syncytial Virus Fusion Glycoprotein in Complex with Neutralizing Antibody 101F
Authors: McLellan Jason S. , Chen Man , Chang Jung-San , Yang Yongping , Kim Albert , Graham Barney S. , Kwong Peter D.
Published: September 2010

Respiratory syncytial virus (RSV) is a major cause of pneumonia and bronchiolitis in infants and elderly people. Currently there is no effective vaccine against RSV, but passive prophylaxis with neutralizing antibodies reduces hospitalizations. To investigate the mechanism of antibody-mediated RSV neutralization, we undertook structure-function studies of monoclonal antibody 101F, which binds a linear epitope in the RSV fusion glycoprotein. Crystal structures of the 101F antigen-binding fragment in complex with peptides from the fusion glycoprotein defined both the extent of the linear epitope and the interactions of residues that are mutated in antibody escape variants. The structure allowed for modeling of 101F in complex with trimers of the fusion glycoprotein, and the resulting models suggested that 101F may contact additional surfaces located outside the linear epitope. This hypothesis was supported by surface plasmon resonance experiments that demonstrated 101F bound the peptide epitope ∼16,000-fold more weakly than the fusion glycoprotein. The modeling also showed no substantial clashes between 101F and the fusion glycoprotein in either the pre- or postfusion state, and cell-based assays indicated that 101F neutralization was not associated with blocking virus attachment. Collectively, these results provide a structural basis for RSV neutralization by antibodies that target a major antigenic site on the fusion glycoprotein.
Endovascular management of spinal dural arteriovenous fistulas
Authors: Patsalides Athos , Santillan Alejandro , Knopman Jared , Tsiouris Apostolos J , Riina Howard A , Gobin Y Pierre
Published: September 2010

Spinal dural arteriovenous fistulas (SDAVFs) represent the most frequent spinal arteriovenous malformation and have an ominous natural history if left untreated. In the present review, we describe the spinal vascular anatomy, pathophysiology and clinical manifestations of SDAVFs, and the current role of endovascular embolization in this type of lesion.
ENTANGLEMENT DYNAMICS OF TWO QUBITS COUPLED TO SQUEEZED DISSIPATIVE ENVIRONMENTS
Authors: SHAN CHUAN-JIA , CHEN TAO , LIU JI-BING , CHENG WEI-WEN , LIU TANG-KUN , HUANG YAN-XIA , LI HONG
Published: September 2010

By analytically solving the Lindblad form of the master equation, we investigate entanglement dynamics of two qubits coupled via the XY interaction, where each qubit is interacting with an independent reservoir with the squeezing parameters and squeezing angles. In the weak-squeezed reservoir, we show that the entanglement sudden death and entanglement sudden birth will happen for various entangled states. Some initial product states evolve into entangled ones, initially entangled states lose completely or partially their entanglement. The effects of varying the degree of entanglement of the initial states, the spin chain system parameters and different values of the degree of squeezing on the sudden death, revival and birth times are analyzed in detail. We also see that the steady state concurrence appears in the squeezed dissipative environments, which is affected by both the system parameters and the degree of squeezing.
NANOMATERIALS UNDER HIGH TEMPERATURE AND HIGH PRESSURE
Authors: KUMAR R. , SHARMA UMA D. , KUMAR MUNISH
Published: September 2010

Two different approaches to study thermal expansion and compression of nanosystems are unified, which have been treated quite independently by earlier workers. We provide the simple theoretical analysis, which demonstrates that these two approaches may be unified into a single theory, viz. one can be derived from other. It is concluded that there is a single theory in the place of two different approaches. To show the real connection with the nanomaterials, we study the effect of temperature (at constant pressure), the effect of pressure (at constant temperature) as well as the combined effect of pressure and temperature. We have considered different nanomaterials viz. carbon nanotube, AlN , Ni , 80 Ni –20 Fe , Fe – Cu , MgO , CeO2, CuO and TiO2. The results obtained are compared with the available experimental data. A good agreement between theory and experiment demonstrates the validity of the present approach.
THIRD-ORDER NONLINEAR OPTICAL PROPERTIES OF [C7H7(C2H5)3N][Ni(dmit)2] USING Z-SCAN TECHNIQUE
Authors: CHEN JING-WEI , REN QUAN , WANG XIN-QIANG , FAN HE-LIANG , SUN QIANG
Published: September 2010

A novel dmit 2- complex: [ C 7 H 7( C 2 H 5)3 N ][ Ni ( dmit )2], abbreviated as BTEANDT, was synthesized and its third-order nonlinear optical properties were investigated by Z-scan technique at the wavelength of 1064 nm with laser duration of 20 ps. A self-focusing effect and a saturable absorption were observed. The nonlinear refraction coefficient n2 and the nonlinear absorption coefficient β have been found to be 7.311 × 10-18 m 2/W and -6.064 cm/GW when I0=3.025 GW/cm2. The intensity dependence curve of β was also studied and the result reveals that β is proportional to I0. We explained the result with the theory of absorption cross-section.
POOL–FRENKEL EFFECT IN POLAR LIQUIDS PLACED IN STRONG ELECTRIC FIELDS
Authors: BORISOV V. S.
Published: September 2010

Specific features of field-enhanced ionization of a polar liquid in the presence of strong electric field are discussed. Within the framework of the developed theory, an equation describing stretching deformation of a homeopolar molecule caused by the external field has been obtained. Numerical analysis of the equation has made it possible to investigate the dependence of molecular relative deformation, binding energy and degree of dissociation on the strength of the electric field. Van der Waals forces reduction in the considered molecule under the influence of external electric field provides noticeable increase in the concentration of ions which formation is due to Pool–Frenkel effect. It has been found that even in the case of weak field Pool–Frenkel effect in a polar liquid is a substantially nonlinear phenomenon.
COOPER PAIR BREAKING
Authors: FULDE P.
Published: September 2010

An overview is given of a number of pair-breaking interactions in superconductors. They have in common that they violate a symmetry of the pair state. In most cases pairs are formed from time reversed single-particle states, a noticeable exception being antiferromagnetic superconductors. When time reversibility is broken by an interaction acting on the electrons, the time evolution of the time-reversal operator plays an important role. Depending on whether it is nonergodic or ergodic, we deal with pair weakening or pair breaking. Numerous different interactions are analyzed and discussed. Unifying features of different pair-breaking cases are pointed out. Special attention is paid to the Zeeman effect and to scattering centers with low-energy excitations. The Kondo effect and crystalline field split rare-earth ions belong in that category. Modifications caused by strongly anisotropic pair states are pointed out. There is strong evidence that in some cases intra-atomic excitations lead to pair formation rather than pair breaking for which an explanation is provided.
ALGEBRAICALLY EXPANDABLE CLASSES OF IMPLICATION ALGEBRAS
Authors: CAMPERCHOLI MIGUEL
Published: September 2010

An algebraically expandable class is a class of algebras axiomatizable by a set of sentences of the form ∀∃! ∧ p = q. We find all algebraically expandable classes in the variety of implication algebras. A representation result for finite implication algebras is proved, and we also give a characterization of the class of congruence permutable implication algebras.
THE STRUCTURE OF THE UNIT GROUP OF THE GROUP ALGEBRA OF PAULI'S GROUP OVER ANY FIELD OF CHARACTERISTIC 2
Authors: GILDEA JOE
Published: September 2010

The structure of the unit group of the group algebra of Pauli's group over any field of characteristic 2 is established in terms of split extensions of cyclic groups.
NON-ADIABATIC GRAVITATIONAL COLLAPSE OF A SUPERDENSE STAR
Authors: SARWE SANJAY , TIKEKAR RAMESH
Published: September 2010

The relativistic equations governing the non-adiabatic shear-free collapse of massive superdense stars in the presence of dissipative forces producing heat flow in the background of space–times of the Vaidya–Tikekar ansatz with associated physical three-spaces that have the three-spheroidal geometry are formulated. It is shown how the system can be used to examine the development and progress of the collapse during subsequent epochs until the radiating star becomes a black hole.
A CLASS OF GUP SOLUTIONS IN DEFORMED QUANTUM MECHANICS
Authors: PEDRAM POURIA
Published: September 2010

Various candidates of quantum gravity such as string theory, loop quantum gravity and black hole physics all predict the existence of a minimum observable length which modifies the Heisenberg uncertainty principle to the so-called generalized uncertainty principle (GUP). This approach results from the modification of the commutation relations and changes all Hamiltonians in quantum mechanics. In this paper, we present a class of physically acceptable solutions for a general commutation relation without directly solving the corresponding generalized Schrödinger equations. These solutions satisfy the boundary conditions and exhibit the effect of the deformed algebra on the energy spectrum. We show that this procedure prevents us from doing equivalent but lengthy calculations.
BiMFG: BIOINFORMATICS TOOLS FOR MARINE AND FRESHWATER SPECIES
Authors: SHIH TSAN-HUANG , CHEN CHIEN-MING , WANG HSIN-WEI , PAI TUN-WEN , CHANG HAO-TENG
Published: September 2010

Biomolecule sequences and structures of land, air and water species are determined rapidly and the data entries are unevenly distributed for different organisms. It frequently leads to the BLAST results of homologous search containing undesirable entries from organisms living in different environments. To reduce irrelevant searching results, a separate database for comparative genomics is urgently required. A comprehensive bioinformatics tool set and an integrated database, named Bioinformatics tools for Marine and Freshwater Genomics (BiMFG), are constructed for comparative analyses among model species and underwater species. Novel matching techniques based on conserved motifs and/or secondary structure elements are designed for efficiently and effectively retrieving and aligning remote sequences through cross-species comparisons. It is especially helpful when sequences under analysis possess low similarities and unresolved structural information. In addition, the system provides core techniques of multiple sequence alignment, multiple second structure profile alignment and iteratively refined multiple structural alignments for biodiversity analysis and verification in marine and freshwater biology. The BiMFG web server is freely available for use at .
EFFICIENT MINING OF HAPLOTYPE PATTERNS FOR LINKAGE DISEQUILIBRIUM MAPPING
Authors: LIN LI , WONG LIMSOON , LEONG TZE-YUN , LAI POH SAN
Published: September 2010

Effective identification of disease-causing gene locations can have significant impact on patient management decisions that will ultimately increase survival rates and improve the overall quality of health care. Linkage disequilibrium mapping is the process of finding disease gene locations through comparisons of haplotype frequencies between disease chromosomes and normal chromosomes. This work presents a new method for linkage disequilibrium mapping. The main advantage of the proposed algorithm, called LinkageTracker, is its consistency in producing good predictive accuracy under different conditions, including extreme conditions where the occurrence of disease samples with the mutation of interest is very low and there is presence of error or noise. We compared our method with some leading methods in linkage disequilibrium mapping such as HapMiner, Blade, GeneRecon, and Haplotype Pattern Mining (HPM). Experimental results show that for a substantial class of problems, our method has good predictive accuracy while taking reasonably short processing time. Furthermore, LinkageTracker does not require any population ancestry information about the disease and the genealogy of the haplotypes. Therefore, it is useful for linkage disequilibrium mapping when the users do not have such information about their datasets.
FUNCTIONAL CLASSIFICATION OF PROTEIN 3D STRUCTURES FROM PREDICTED LOCAL INTERACTION SITES
Authors: PARASURAM RAMYA , LEE JOSLYNN S. , YIN PENGCHENG , SOMAROWTHU SRINIVAS , ONDRECHEN MARY JO
Published: September 2010

A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.
ISOFORM ABUNDANCE INFERENCE PROVIDES A MORE ACCURATE ESTIMATION OF GENE EXPRESSION LEVELS IN RNA-SEQ
Authors: WANG XI , WU ZHENGPENG , ZHANG XUEGONG
Published: September 2010

Due to its unprecedented high-resolution and detailed information, RNA-seq technology based on next-generation high-throughput sequencing significantly boosts the ability to study transcriptomes. The estimation of genes' transcript abundance levels or gene expression levels has always been an important question in research on the transcriptional regulation and gene functions. On the basis of the concept of Reads Per Kilo-base per Million reads (RPKM), taking the union-intersection genes (UI-based) and summing up inferred isoform abundance (isoform-based) are the two current strategies to estimate gene expression levels, but produce different estimations. In this paper, we made the first attempt to compare the two strategies' performances through a series of simulation studies. Our results showed that the isoform-based method gives not only more accurate estimation but also has less uncertainty than the UI-based strategy. If taking into account the non-uniformity of read distribution, the isoform-based method can further reduce estimation errors. We applied both strategies to real RNA-seq datasets of technical replicates, and found that the isoform-based strategy also displays a better performance. For a more accurate estimation of gene expression levels from RNA-seq data, even if the abundance levels of isoforms are not of interest, it is still better to first infer the isoform abundance and sum them up to get the expression level of a gene as a whole.
G6PD-MutDB: A MUTATION AND PHENOTYPE DATABASE OF GLUCOSE-6-PHOSPHATE (G6PD) DEFICIENCY
Authors: ZHAO XIN , LI ZUOFENG , ZHANG XIAOYAN
Published: September 2010

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common hereditary enzymatic disorder of red blood cells in humans due to mutations in the G6PD gene. The G6PD enzyme catalyzes the first step in the pentose phosphate pathway to protect cells against oxidative stress. Mutations in the G6PD gene will cause functional variants with various biochemical and clinical phenotypes. So far, about 160 mutations along with more than 400 biochemical variants have been described. G6PD-MutDB is a disease-specific resource of G6PD deficiency, collecting and integrating G6PD mutations with biochemical and clinical phenotypes. Data of G6PD deficiency is manually extracted from published papers, focusing primarily on variants with identified mutation and well-described quantitative phenotypes. G6PD-MutDB implements an approach, CNSHA predictor, to help identify a potential chronic non-spherocytic hemolytic anemia (CNSHA) phenotype of an unknown mutation. G6PD-MutDB is believed to facilitate analysis of relationship between molecular mutation and functional phenotype of G6PD deficiency owing to convenient data resource and useful tools. This database is available from .
DIGOUT: VIEWING DIFFERENTIAL EXPRESSION GENES AS OUTLIERS
Authors: YU HUI , TU KANG , XIE LU , LI YUAN-YUAN
Published: September 2010

With regards to well-replicated two-conditional microarray datasets, the selection of differentially expressed (DE) genes is a well-studied computational topic, but for multi-conditional microarray datasets with limited or no replication, the same task is not properly addressed by previous studies. This paper adopts multivariate outlier analysis to analyze replication-lacking multi-conditional microarray datasets, finding that it performs significantly better than the widely used limit fold change (LFC) model in a simulated comparative experiment. Compared with the LFC model, the multivariate outlier analysis also demonstrates improved stability against sample variations in a series of manipulated real expression datasets. The reanalysis of a real non-replicated multi-conditional expression dataset series leads to satisfactory results. In conclusion, a multivariate outlier analysis algorithm, like DigOut, is particularly useful for selecting DE genes from non-replicated multi-conditional gene expression dataset.
ENVIRONMENTAL DEPENDENCY OF GENE KNOCKOUTS ON PHENOTYPE MICROARRAY ANALYSIS IN ESCHERICHIA COLI
Authors: TOHSATO YUKAKO , BABA TOMOYA , MAZAKI YUSAKU , ITO MASAHIRO , WANNER BARRY L. , MORI HIROTADA
Published: September 2010

Systematic studies have revealed that single gene deletions often display little phenotypic effects under laboratory conditions and that in many cases gene dispensability depends on the experimental conditions. To elucidate the environmental dependency of genes, we analyzed the effects of gene deletions by Phenotype MicroArray™ (PM), a system for quantitative screening of thousands of phenotypes in a high-throughput manner. Here, we proposed a new statistical approach to minimize error inherent in measurements of low respiration rates and find which mutants showed significant phenotypic changes in comparison to the wild-type. We show analyzing results from comprehensive PM assays of 298 single-gene knockout mutants in the Keio collection and two additional mutants under 1,920 different conditions. We focused on isozymes of these genes as simple duplications and analyzed correlations between phenotype changes and protein expression levels. Our results revealed divergence of the environmental dependency of the gene among the knockout genes and have also given some insights into possibilities of alternative pathways and availabilities of information on protein synthesis patterns to classify or predict functions of target genes from systematic phenotype screening.
QUANTUM KEY DISTRIBUTION WITH FOUR ALPHABETIC LETTERS NON-GAUSSIAN MODULATION USING SQUEEZING STATES
Authors: ZHANG SHENG , WANG JIAN , TANG CHAO-JING , ZHANG QUAN
Published: September 2010

We present a new non-Gaussian quantum key distribution (QKD) protocol using squeezed states. Compared with a binary modulation, the efficiency can be improved when a four alphabetic letters modulation is chosen. We then analyze the security of the protocol under a collective entangling cloner attack, which is a powerful attack strategy in continuous variable QKD. We also show how the modulation coefficient affects the key rate, then the key rate can be maximized by choosing an optimal coefficient.
QUANTUM HITTING TIME ON THE COMPLETE GRAPH
Authors: SANTOS RAQUELINE AZEVEDO MEDEIROS , PORTUGAL RENATO
Published: September 2010

Quantum walks play an important role in the area of quantum algorithms. Many interesting problems can be reduced to searching marked states in a quantum Markov chain. In this context, the notion of quantum hitting time is very important, because it quantifies the running time of the algorithms. Markov chain-based algorithms are probabilistic, therefore the calculation of the success probability is also required in the analysis of the computational complexity. Using Szegedy's definition of quantum hitting time, which is a natural extension of the definition of the classical hitting time, we present analytical expressions for the hitting time and success probability of the quantum walk on the complete graph.