bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Diet Crossover to Determine the Effects of β‐glucan Supplementation on Immunity and Growth of Nile Tilapia, Oreochromis niloticus
Authors: Welker Thomas L. , Lim Chhorn , Yildirim‐Aksoy Mediha , Klesius Phillip H.
Published: June 2012

Juvenile Nile tilapia were fed either a basal (control) diet (n = 6 aquaria) or a diet supplemented with 1 g/kg β‐glucan (n = 24 aquaria) for 4 wk. At the end of this period, fish receiving β‐glucan were continued on the same diet (n = 12 aquaria) or switched to the control diet (n = 12 aquaria) for 2 wk. After 6 wk, tilapia continuously fed the β‐glucan supplemented diets had improved weight gain and feed efficiency than those fed the control diet uninterrupted or switched from the β‐glucan diet to the control after 4 wk. Feeding tilapia β‐glucan for 4 wk and then switching to the basal diet for 2 wk caused a significant increase in the respiratory burst of polymorphonuclear lymphocytes (17.77 × 103 units/1000 white blood cells [WBC]) compared to catfish fed the control diet (13.50 × 103 units/1000 WBC) or the β‐glucan diet continuously (13.57 × 103 units/1000 WBC), but other immune parameters were unaffected. Tilapia were then challenged with Streptococcus iniae. The two groups were divided again (n = 6 aquaria) postchallenge and continued on the same diet or switched to the other diet (β‐glucan or control) for another 3 wk. No differences in survival to S. iniae infection occurred between dietary groups.
Sex determination meltdown upon biological control introduction of the parasitoid Cotesia rubecula?
Authors: de Boer Jetske G. , Kuijper Bram , Heimpel George E. , Beukeboom Leo W.
Published: June 2012

Natural enemies may go through genetic bottlenecks during the process of biological control introductions. Such bottlenecks are expected to be particularly detrimental in parasitoid Hymenoptera that exhibit complementary sex determination (CSD). CSD is associated with a severe form of inbreeding depression because homozygosity at one or multiple sex loci leads to the production of diploid males that are typically unviable or sterile. We observed that diploid males occur at a relatively high rate (8–13% of diploid adults) in a field population of
Cotesia rubecula in Minnesota, USA, where this parasitoid was introduced for biological control of the cabbage white
Pieris rapae. However, our laboratory crosses suggest two‐locus CSD in a native Dutch population of
C. rubecula and moderately high diploid males survival (approximately 70%), a scenario expected to produce low proportions of diploid males. We also show that courtship behavior of diploid males is similar to that of haploid males, but females mated to diploid males produce only very few daughters that are triploid. We use our laboratory data to estimate sex allele diversity in the field population of
C. rubecula and discuss the possibility of a sex determination meltdown from two‐locus CSD to effective single‐locus CSD during or after introduction.
Reproductive success of captively bred and naturally spawned Chinook salmon colonizing newly accessible habitat
Authors: Anderson Joseph H. , Faulds Paul L. , Atlas William I. , Quinn Thomas P.
Published: June 2012

Captively reared animals can provide an immediate demographic boost in reintroduction programs, but may also reduce the fitness of colonizing populations. Construction of a fish passage facility at Landsburg Diversion Dam on the Cedar River, WA, USA, provided a unique opportunity to explore this trade‐off. We thoroughly sampled adult Chinook salmon (Oncorhynchus tshawytscha) at the onset of colonization (2003–2009), constructed a pedigree from genotypes at 10 microsatellite loci, and calculated reproductive success (RS) as the total number of returning adult offspring. Hatchery males were consistently but not significantly less productive than naturally spawned males (range in relative RS: 0.70–0.90), but the pattern for females varied between years. The sex ratio was heavily biased toward males; therefore, inclusion of the hatchery males increased the risk of a genetic fitness cost with little demographic benefit. Measurements of natural selection indicated that larger salmon had higher RS than smaller fish. Fish that arrived early to the spawning grounds tended to be more productive than later fish, although in some years, RS was maximized at intermediate dates. Our results underscore the importance of natural and sexual selection in promoting adaptation during reintroductions.
Magnesium Reduces Carotid Intima‐Media Thickness in a Mouse Model of Pseudoxanthoma Elasticum: A Novel Treatment Biomarker
Authors: Kupetsky‐Rincon Erine A. , Li Qiaoli , Uitto Jouni
Published: June 2012

Pseudoxanthoma elasticum (PXE), which demonstrates progressive build‐up of calcium phosphate and proteoglycan deposits in skin, eye, and arteries, has been associated with myocardial infarctions, stroke, and blindness. In a mouse model of PXE, a magnesium‐enriched diet prevents mineralization of the vibrissae capsule, an early biomarker for PXE. However, biomarkers for therapeutic responses in PXE have not been identified in humans. Because PXE patients have an increased carotid intima‐media thickness (CIMT), a risk factor for cardiovascular disease and stroke, we analyzed the feasibility of CIMT as a treatment endpoint before and after magnesium supplementation in a mouse model of PXE (Abcc6−/−). CIMT was measured in 1‐year‐old Abcc6−/− and Abcc6+/+ mice fed either standard rodent diet with or without magnesium oxide supplementation for 2 months. Baseline CIMT in Abcc6−/− versus Abcc6+/+ mice was increased (p value = 0.009), whereas CIMT in magnesium‐treated versus untreated Abcc6−/− mice was reduced (p value = 0.024). CIMT is a novel treatment endpoint in this mouse model and may serve as a predictive biomarker of therapeutic response in PXE patients. In that context, magnesium oxide significantly reduced CIMT in PXE mice, and may be useful for disease prevention in PXE patients. Clin Trans Sci 2012; Volume #: 1–6
Does Metformin Increase Paraoxonase Activity in Patients with the Metabolic Syndrome? Additional Data from the MEFISTO Study
Authors: Meaney Eduardo , Sierra‐Vargas Patricia , Meaney Alejandra , Guzmán‐Grenfell Martín , Ramírez‐Sánchez Israel , Hicks Juan Jose , Olivares‐Corichi Ivonne , Ceballos Guillermo
Published: June 2012

In a subanalysis on the metformin, arterial function, intima‐media thickness, and nitroxidation in the metabolic syndrome (MEFISTO)8 (an open‐label fashion, with 1 year of 850 mg daily of metformin) subjects’ samples, we measured the paraoxonase 1 (PON1) activity in 39 patients that finished the study and relate values with high density lipoprotein (HDL). The comparative PON1 activities at the beginning and at the end of the study were 5.528 ± 0.588 and 4.743 ± 0.619 nmol/mg protein/min (NS) for control group and 3.229 ± 0.403 and 5.135 ± 0.585 nmol/mg protein/min (p < 0.02) for the metformin group. Our data showed an enhance of PON1 activity in patients with metabolic syndrome treated with metformin, although in them, the raise of HDL concentration was less than control patients, suggesting that the increase in quality (measured here as PON1 activity) could be at least as important as an increase in its concentration. Our results point out that there is a relationship among PON1 activity and the reduction of carotideal intima‐media thickness. Clin Trans Sci 2012; Volume #: 1–4
Marine population connectivity identifies ecological neighbors for conservation planning in the Coral Triangle
Authors: Treml Eric A. , Halpin Patrick N.
Published: June 2012

Robust conservation plans seek to accommodate functional connectivity by establishing regional priorities and through decisions regarding the size and placement of protected areas. In marine systems, connectivity refers to the ecological linkages (primarily larval dispersal) between populations and protected areas. Unfortunately, connectivity data for the majority of populations are unavailable, requiring managers to rely on expert knowledge and general "scale" and "distance" guidelines. We present a novel approach for integrating model‐based connectivity estimates into the conservation planning framework. We quantify multispecies connectivity across the Indo‐Pacific and demonstrate how this informs conservation planning in the Coral Triangle across three levels: countries, ecoregions, and priority seascapes. The emergent network structure of ecological linkages between planning regions complements the current bioregionalization across the Coral Triangle. This new ecological network perspective will help (re)define partnerships and assist in coordinating policy actions, ultimately leading to a more effective planning process.
Cardiac Troponin I in Calves with Congenital Heart Disease
Authors: Suzuki K. , Uchida E. , Schober K. E. , Niehaus A. , Rings M. D. , Lakritz J.
Published: June 2012

Background

The association between plasma cardiac troponin I (cTnI) and the magnitude of cardiac enlargement in calves with congenital heart disease (CHD) are not well defined.

Objective

To investigate the relationship between plasmacTnIconcentrations and cardiac size in healthy calves and calves withCHD.

Animals

A total of 19 healthy calves (control) and 12 Holstein calves withCHD(patent ductus arteriosus, ventricular septal defect, tetralogy of Fallot or double outlet right ventricle).

Methods

Case control study. All animals underwent a comprehensive transthoracic echocardiographic study to document cardiac health or presence ofCHD. The vertebral heart score (VHS) was determined in each animal using right lateral survey radiographic images. Blood samples were collected via jugular venipuncture and plasmacTnIconcentration and creatine kinase (CK) activity were determined by a 3rd generation immunoassay and an automatic biochemical analyzer, respectively. Groups were compared usingMann‐WhitneyU‐test and receiver‐operating characteristics (ROC) curve analysis.

Results

Calves withCHDhad significantly largerVHSvalues and higher plasmacTnIconcentrations (P < .001) compared to control. Creatine kinase activity was not different between the control andCHDgroups of calves. Diagnostic cutoffs ofVHSand plasmacTnIfor discrimination of groups were 8.9 vertebrae and 0.035 ng/mL, respectively. ThecTnIconcentration in plasma was significantly correlated withVHS(r2=0.512,P < .001).

Conclusion and Clinical Relevance

Our results suggest that determination of plasmacTnIconcentrations in calves with clinical signs compatible withCHDmight prove useful as a guide to quantify cardiac remodeling associated with increased cardiac size.
Beyond sensitivity: nonlinear perturbation analysis of transient dynamics
Authors: Stott Iain , Hodgson David James , Townley Stuart
Published: June 2012

1. Perturbation analyses of population models are integral to population management: such analyses evaluate how changes in vital rates of members of the population translate to changes in population dynamics. Sensitivity and elasticity analyses of long‐term (asymptotic) growth are popular, but limited: they ignore short‐term (transient) dynamics and provide a linear approximation to nonlinear perturbation curves.

2. Population inertia measures how much larger or smaller a non‐stable population becomes compared with an equivalent stable population, as a result of transient dynamics. We present formulae for the transfer function of population inertia, which describes nonlinear perturbation curves of transient population dynamics. The method comfortably fits into wider frameworks for analytical study of transient dynamics, and for perturbation analyses that use the transfer function approach.

3. We use case studies to illustrate how the transfer function of population inertia may be used in population management. These show that strategies based solely on asymptotic perturbation analyses can cause undesirable transient dynamics and/or fail to exploit desirable transient dynamics. This highlights the importance of considering both transient and asymptotic population dynamics in population management.

4. Our case studies also show a tendency towards marked nonlinearity in transient perturbation curves. We extend our method to measure sensitivity of population inertia and show that it often fails to capture dynamics resulting from perturbations typical of management scenarios.
A mechanistic pharmacokinetic model to assess modified oral drug bioavailability post bariatric surgery in morbidly obese patients: interplay between CYP3A gut wall metabolism, permeability and dissolution
Authors: Darwich Adam S , Pade Devendra , Ammori Basil J , Jamei Masoud , Ashcroft Darren M , Rostami-Hodjegan Amin
Published: June 2012

Objectives

Due to the multi-factorial physiological implications of bariatric surgery, attempts to explain trends in oral bioavailability following bariatric surgery using singular attributes of drugs or simplified categorisations such as the biopharmaceutics classification system have been unsuccessful. So we have attempted to use mechanistic models to assess changes to bioavailability of model drugs.

Methods

Pharmacokinetic post bariatric surgery models were created for Roux-en-Y gastric bypass, biliopancreatic diversion with duodenal switch, sleeve gastrectomy and jejunoileal bypass, through altering the ‘Advanced Dissolution Absorption and Metabolism’ (ADAM) model incorporated into the Simcyp® Simulator. Post to pre surgical simulations were carried out for five drugs with varying characteristics regarding their gut wall metabolism, dissolution and permeability (simvastatin, omeprazole, diclofenac, fluconazole and ciprofloxacin).

Key findings

The trends in oral bioavailability pre to post surgery were found to be dependent on a combination of drug parameters, including solubility, permeability and gastrointestinal metabolism as well as the surgical procedure carried out.

Conclusions

In the absence of clinical studies, the ability to project the direction and the magnitude of changes in bioavailability of drug therapy, using evidence-based mechanistic pharmacokinetic in silico models would be of significant value in guiding prescribers to make the necessary adjustments to dosage regimens for an increasing population of patients who are undergoing bariatric surgery.
The benefits of pharmacist-delivered warfarin education in the home
Authors: Stafford Leanne , van Tienen Ella C , Bereznicki Luke R E , Peterson Gregory M
Published: June 2012

Objectives

Good warfarin knowledge is important for optimal patient outcomes, but barriers exist to effective education and warfarin knowledge is often poor. This study aimed to explore the educational outcomes of home-based warfarin education provided by trained pharmacists.

Methods

In a prospective, non-randomised, controlled cohort trial, patients received either usual community-based post-discharge care or a post-discharge warfarin management service, including warfarin education by trained pharmacists during two or three home visits. Patients’ warfarin knowledge was assessed at 8 and 90 days post-discharge using the Oral Anticoagulation Knowledge test.

Key findings

One hundred and thirty-nine patients were recruited into the usual care group between November 2008 and August 2009, and 129 into the intervention group between May and December 2009. Pharmacist-delivered warfarin education was associated with a significant difference between the intervention patients’ baseline and day 8 mean warfarin knowledge scores of 64.5% (95% confidence interval (CI) 61.0–68.5%) and 78.0% (95% CI 74.5–81.5%; P < 0.001), respectively. The intervention patients also scored significantly higher than the usual care patients at day 8 (65.0%, 95% CI 61.5–68.0%; P < 0.001), but not at day 90.

Conclusions

Use of an existing healthcare framework overcame several systemic barriers by facilitating warfarin education in patients’ homes. While the intervention was associated with better short-term warfarin knowledge, follow-up may be required to optimise its benefits. Widespread implementation of home-based warfarin education by pharmacists has the potential to contribute significantly to improved outcomes from warfarin therapy.
Experimental and Numerical Investigation of Combustor-Turbine Interaction Using an Isothermal, Nonreacting Tracer
Authors: Cha Chong M. , Hong Sungkook , Ireland Peter T. , Denman Paul , Savarianandam Vivek
Published: June 2012

Understanding the interaction between the combustor and turbine subsystems of a gas turbine engine is believed to be key in developing focused strategies for improving turbine performance. Past studies have approached the problem starting with an existing turbine rig with inlet conditions provided by “representative” hardware which attempts to mimic some key flow features exiting the combustor. In this paper, experiments are performed which center around complete engine hardware of the combustor, including engine geometry turbine nozzle guide vanes (NGVs) to solely represent the upstream impact of the complete turbine. This domain ensures that the traditional interface between combustor and turbine is sufficiently encompassed and not compromised by obfuscating or limiting effects due to approximating combustor hardware. The full-annular experimental measurements include all components of the velocity and pressure fields at various planar sections perpendicular to the primary flow direction. These include detailed, two-dimensional measurements both upstream and downstream of the NGVs. The combustor is a classic rich-burn design. Passive scalar (CO2) tracing measurements are performed to gain insight into the flow responsible for the temperature fields in the coupled system, including the impact of the NGVs on the upstream flow at the conventional combustor-turbine interface. CFD simulations are used to develop a complete picture of the combustor-turbine interface and the coupling between the two subsystems. The complementary experimental and simulation datasets are together intended to provide a benchmark for future, more traditional turbine rig tests and turbine CFD simulations where inlet conditions are at the exit plane of the combustor.
Detached Eddy Simulation of Free-Surface Flow Around a Submerged Submarine Fairwater
Authors: Ikram Z. , Avital E. J. , Williams J. J. R.
Published: June 2012

The effects of reducing submergence depth around a submerged submarine fairwater without its associated appendages is numerically studied using detached eddy simulation. The submerged body is modeled using the ghost-cell immersed boundary method, while the free-surface is accounted for by using a moving mesh. The numerical simulations are performed at a Reynolds number of 11 × 106 for a submergence ratio in the range of 0.44–0.32 and for Froude numbers <1. This paper examines the effect of depth variation on the statistical and structural behavior of the flow around a fully submerged fairwater. The results include profiles of the time averaged velocity, turbulent intensities, turbulent kinetic energy spectra and budget. These have all shown that the major part of the turbulence is confined to the near wake region of the fairwater. Vortical structures are found to show no significant rise or interaction with the free-surface, while in the wake region, the results show that vorticity is present for over 50% of the total monitored period. Reducing the submergence depth is found to influence the tip vortex shedding. Additionally, time averaged forces, force variations, and shedding frequency are also examined. In all cases, the surface waves generated by the submerged fairwater are of a Kelvin kind.
Draft Genome Sequence of Bacillus cereus Strain LCT-BC244
Authors: Su Longxiang , Zhou Tao , Zhou Lisha , Fang Xiangqun , Li Tianzhi , Wang Junfeng , Guo Yinghua , Chang De , Wang Yajuan , Li Dongfang , Liu Changting
Published: June 2012

Bacillus cereus
is a prevalent, soil-dwelling, Gram-positive bacterium. Some strains are harmful to humans and cause food-borne illness, while other strains can be beneficial as probiotics for animals. To gain insight into the bacterial genetic determinants, we report the genome sequence of a strain, LCT-BC244, which was isolated from CGMCC 1.230.
Genome Sequence of “Candidatus Aquiluna” sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord
Authors: Kang Ilnam , Lee Kiyoung , Yang Seung-Jo , Choi Ahyoung , Kang Dongmin , Lee Yoo Kyoung , Cho Jang-Cheon
Published: June 2012

We report the genome sequence of actinobacterial strain IMCC13023, isolated from arctic fjord seawater. Phylogenetic analysis of 16S rRNA gene showed that the strain is related to “
Candidatus
Aquiluna rubra.” The genome information suggests that strain IMCC13023 is a photoheterotroph carrying actinorhodopsin, with the smallest genome ever reported for a free-living member of the
Actinobacteria
.
Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain
Authors: Lira Felipe , Hernández Alvaro , Belda Eugeni , Sánchez María B. , Moya Andrés , Silva Francisco J. , Martínez José L.
Published: June 2012

Stenotrophomonas maltophilia
is an opportunistic pathogen with an environmental origin, and it is an increasingly relevant cause of nosocomial infections. Here we present the whole-genome sequence of
S. maltophilia
strain D457, a clinical isolate that is being used as a model for studying antibiotic resistance in this bacterial species.
Genome Sequence of a Novel Nicotine-Degrading Strain, Pseudomonas geniculata N1
Authors: Tang Hongzhi , Yu Hao , Tai Cui , Huang Kaiming , Liu Yanghui , Wang Lijuan , Yao Yuxiang , Wu Geng , Xu Ping
Published: June 2012

A newly isolated bacterium,
Pseudomonas geniculata
N1, can efficiently degrade nicotine. Here we present a 4.51-Mb assembly of its genome, which is the first sequence of the
P. geniculata
group. The sequence contains the genes related to nicotine catabolism and may provide insights into its molecular mechanism for N-heterocyclic degradation.
Protein Export According to Schedule: Architecture, Assembly, and Regulation of Type III Secretion Systems from Plant- and Animal-Pathogenic Bacteria
Authors: Büttner Daniela
Published: June 2012

Flagellar and translocation-associated type III secretion (T3S) systems are present in most Gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.
Diversity in GeneticIn VivoMethods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System
Authors: Stynen Bram , Tournu Hélène , Tavernier Jan , Van Dijck Patrick
Published: June 2012

The yeast two-hybrid system pioneered the field ofin vivoprotein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to studyin vivobinary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such asSaccharomyces cerevisiaeandEscherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
TWO NEW SERVICING STRATEGIES FOR PRODUCTS SOLD WITH WARRANTY
Authors: ISKANDAR BERMAWI P. , JACK NAT , MURTHY D. N. PRA
Published: June 2012

For a repairable product that fails under warranty, the manufacturer can choose between repair and replacement. Many different warranty servicing strategies involving these two types of rectification action have already been studied. In this paper, we propose two new servicing strategies involving minimal repair, each with two parameters that are selected optimally to minimize expected warranty servicing costs. We develop models to obtain the optimal parameter values for each new strategy and then carry out a comparison with a selection of the existing strategies through a numerical example.
A DERIVATION OF THE WEYL ORDERED FORM OF TWO-MODE FRESNEL OPERATOR BY VIRTUE OF THE WEYL OPERATOR ORDERING METHOD
Authors: REN GANG , DU JIAN-MING
Published: June 2012

Based on the technique of integration with a Weyl ordered product (IWWOP) for the two-mode operator, we derive out the Weyl ordered form of two-mode Fresnel operator (TFO). The multiplication rule for TFO and the matrix element of Weyl ordered form of TFO in coordinate eigenstates are also discussed.
RESONANT AC CONDUCTING SPECTRA IN QUASIPERIODIC SYSTEMS
Authors: SANCHEZ VICENTA , WANG CHUMIN
Published: June 2012

Based on the Kubo-Greenwood formula, a renormalization plus convolution method is developed to investigate the frequency-dependent electrical conductivity of quasiperiodic systems. This method combines the convolution theorem with the real-space renormalization technique which is able to address multidimensional systems with 1024 atoms. In this article, an analytical evaluation of the Kubo-Greenwood formula is presented for the ballistic ac conductivity in periodic chains. For quasiperiodic Fibonacci lattices connected to two semi-infinite periodic leads, the electrical conductivity, is calculated by using the renormalization method and the results show that at several frequencies, their ac conductivities could be larger than the ballistic ones. This fact might be related to the resonant scattering process in quasiperiodic systems. Finally, calculations made in segmented Fibonacci nanowires reveal that this improvement to the ballistic ac conductivity via quasiperiodicity is also present in multidimensional systems.
SIMULATION OF COPPER NANOCLUSTER DEPOSITION ON THE CONTAMINATED SURFACE USING GAMING GPU
Authors: OZHGIBESOV M. S. , UTKIN A. V. , FOMIN V. M. , LEU T. S. , CHENG C. H.
Published: June 2012

The purpose of current work was twofold: to compare efficiencies of several different MD algorithms in case of their implementations on CUDA capable GPU and to study effects accompanying a coating process of contaminated copper substrate using CUDA based program. In this paper, we have discussed various aspects of CUDA technology implementation by using the real problem of molecular dynamic simulations as an example. The created CUDA based program allowed us to perform the detailed studies of the physical processes accompanying copper cluster collision with the copper substrate having one-atom layer of carbon in its top surface. It has been defined that the coating cannot be observed if the falling cluster has initial velocity lower than the critical value. Furthermore, the correlation between critical initial velocity and critical value of the angle of incidence of the copper cluster has also been observed. The comparison between execution time of CUDA MD program and MPI program based on one-dimensional parallelization with dynamic load balancing has been performed in the current work.
Parallelization of Belief Propagation on Cell Processors for Stereo Vision
Authors: Hsieh Kun-Yuan , Lai Chi-Hua , Lai Shang-Hong , Lee Jenq Kuen
Published: June 2012

Markov random field models provide a robust formulation for the stereo vision problem of inferring three-dimensional scene geometry from two images taken from different viewpoints. One of the most advanced algorithms for solving the associated energy minimization problem in the formulation is belief propagation (BP). Although BP provides very accurate results in solving stereo vision problems, the high computational cost of the algorithm hinders it from real-time applications. In recent years, multicore architectures have been widely adopted in various industrial application domains. The high computing power of multicore processors provides new opportunities to implement stereo vision algorithms. This article examines and extracts the parallelisms in the BP method for stereo vision on multicore processors. This article shows that parallelism of the algorithm can be efficiently utilized on multicore processors. The results show that parallelization on multicore processors provides a speedup for the BP algorithm of almost 15 times compared to the single-processor implementation on the PPE of the Cell BE. The experimental results also indicate that a frame rate of 6.5 frames/second is possible when implementing the parallelized BP algorithm on the multicore processor of Cell BE with one PPE and six SPEs.
Error-Aware Algorithm/Architecture Coexploration for Video Over Wireless Applications
Authors: Khajeh Amin , Kim Minyoung , Dutt Nikil , Eltawil Ahmed M. , Kurdahi Fadi J.
Published: June 2012

In this article, we propose a cross-layer algorithm/architecture coexploration for wireless multimedia systems to coordinate interactions among sublayer optimizers for improvements in energy/QoS/reliability. By exploiting the inherent redundancy in wireless multimedia systems, we generate an expanded design space over traditional layer-specific approaches. Specifically, we control the error resilient encoder at the application layer to provide awareness of architectural exploration at the physical layer allowing new design points with lower power consumption via aggressive voltage scaling. While trying to reduce energy consumption, the fault tolerant technique compensates the effect of the hardware and network errors due to aggressive voltage scaling and lossy transmission, respectively. Our experiments on H.263 video over a WCDMA communication system demonstrate that coexploration enlarges the feasible design space, which results in significant power savings of more than 20% in the WCDMA modem.
Storage Optimization through Offset Assignment with Variable Coalescing
Authors: Salamy Hassan , Ramanujam J.
Published: June 2012

Most modern digital signal processors (DSPs) provide multiple address registers and a dedicated address generation unit (AGU) which performs address generation in parallel to instruction execution. There is no address computation overhead if the next address is within the auto-modify range. A careful placement of variables in memory is utilized to decrease the number of address arithmetic instructions and thus to generate compact and efficient code. The simple offset assignment (SOA) problem concerns the layout of variables for machines with one address register and the general offset assignment (GOA) deals with multiple address registers. Both these problems assume that each variable needs to be allocated for the entire duration of a program. Both SOA and GOA are NP-complete. In this article, we present effective heuristics for the simple and the general offset assignment problems with variable coalescing where two or more non-interfering variables can be mapped into the same memory location. Results on several benchmarks show the significant improvement of our proposed heuristics compared to other heuristics in the literature.
Incorporating Sentiment Prior Knowledge for Weakly Supervised Sentiment Analysis
Authors: He Yulan
Published: June 2012

This article presents two novel approaches for incorporating sentiment prior knowledge into the topic model for weakly supervised sentiment analysis where sentiment labels are considered as topics. One is by modifying the Dirichlet prior for topic-word distribution (LDA-DP), the other is by augmenting the model objective function through adding terms that express preferences on expectations of sentiment labels of the lexicon words using generalized expectation criteria (LDA-GE). We conducted extensive experiments on English movie review data and multi-domain sentiment dataset as well as Chinese product reviews about mobile phones, digital cameras, MP3 players, and monitors. The results show that while both LDA-DP and LDA-GE perform comparably to existing weakly supervised sentiment classification algorithms, they are much simpler and computationally efficient, rendering them more suitable for online and real-time sentiment classification on the Web. We observed that LDA-GE is more effective than LDA-DP, suggesting that it should be preferred when considering employing the topic model for sentiment analysis. Moreover, both models are able to extract highly domain-salient polarity words from text.
Hedgehog Signaling and Maintenance of Homeostasis in the Intestinal Epithelium
Authors: Büller Nikè V. J. A. , Rosekrans Sanne L. , Westerlund Jessica , van den Brink Gijs R.
Published: June 2012

Homeostasis of the rapidly renewing intestinal epithelium depends on a balance between cell proliferation and loss. Indian hedgehog (Ihh) acts as a negative feedback signal in this dynamic equilibrium. We discuss recent evidence that Ihh may be one of the key epithelial signals that indicates epithelial integrity to the underlying mesenchyme.
Striatal Mechanisms Underlying Movement, Reinforcement, and Punishment
Authors: Kravitz Alexxai V. , Kreitzer Anatol C.
Published: June 2012

Direct and indirect pathway striatal neurons are known to exert opposing control over motor output. In this review, we discuss a hypothetical extension of this framework, in which direct pathway striatal neurons also mediate reinforcement and reward, and indirect pathway neurons mediate punishment and aversion.
The Grasp Reflex and Moro Reflex in Infants: Hierarchy of Primitive Reflex Responses
Authors: Futagi Yasuyuki , Toribe Yasuhisa , Suzuki Yasuhiro
Published: June 2012

The plantar grasp reflex is of great clinical significance, especially in terms of the detection of spasticity. The palmar grasp reflex also has diagnostic significance. This grasp reflex of the hands and feet is mediated by a spinal reflex mechanism, which appears to be under the regulatory control of nonprimary motor areas through the spinal interneurons. This reflex in human infants can be regarded as a rudiment of phylogenetic function. The absence of the Moro reflex during the neonatal period and early infancy is highly diagnostic, indicating a variety of compromised conditions. The center of the reflex is probably in the lower region of the pons to the medulla. The phylogenetic meaning of the reflex remains unclear. However, the hierarchical interrelation among these primitive reflexes seems to be essential for the arboreal life of monkey newborns, and the possible role of the Moro reflex in these newborns was discussed in relation to the interrelationship.
Therapeutic Angiogenesis of PLGA‐Heparin Nanoparticle in Mouse Ischemic Limb
Authors: Lian Lishan , Tang Feng , Yang Jing , Liu Changwei , Li Yongjun
Published: June 2012

Objective. To evaluate the possibility and efficacy of the nanoparticle encapsulating heparin as a novel delivery system to treat ischemic disease. Methods. Firstly, to synthesize the PLGA heparin and test the surface morphology, the average diameter, the loading efficiency, and the release time in vitro, then inject the PLGA heparin into mouse ischemic limbs to observe the perfusion recovery with LDPI at the time of postischemic 7, 14, 21, and 28 days, and, finally, test the expression of VEGF and HGF, the number of the neovessels and record the necrotic score of ischemic limbs. Results. The surface morphology of the PLGA heparin was smooth, the average diameter was 297 nm, the loading efficiency was 5.35%, and the release period maintained for 14 days. In animal experiment, the perfusion recovery, HGF expression level, and capillary density in PLGA‐heparin group were significantly higher than that in control group, and this was consistent with less ischemic limb necrosis. Conclusion. Nanoparticle encapsulating heparin could be successful and efficient in ischemic disease. The therapeutic angiogenesis of PLGA heparin might be due to the prolongation of its biological effects with stimulating growth factor expression.
Effective Sol-Gel Nanocoatings on ZnO Electrodes for Suppressing Recombination in Dye-Sensitized Solar Cells
Authors: Ueno Shintaro , Fujihara Shinobu
Published: June 2012

Attempts have been made to improve the performance of dye-sensitized solar cells by forming metal-oxide nanocoating layers on ZnO electrodes by a sol-gel transformation. SiO2, Nb2O5, TiO2, or ZrO2nanocoating layers could be formed by dipping ZnO films into metal alkoxide solutions of low concentrations and subsequent heat treatments. The performance of DSSCs using the coated ZnO electrodes depends strongly on the structure of coating layers such as the thickness and the surface coverage, which are significantly influenced by the coating conditions. In particular, SiO2and Nb2O5coating layers are effective to suppress the recombination by constructing the energy barrier at the ZnO/electrolyte interface and enhance energy conversion efficiency. It is found that the coating layers also hinder the grain growth of ZnO, contributing to the enhanced cell performance as well.
A Lipocalin-Derived Peptide Modulating Fibroblasts and Extracellular Matrix Proteins
Authors: Carrijo-Carvalho Linda Christian , Maria Durvanei A. , Ventura Janaina S. , Morais Kátia L. P. , Melo Robson L. , Rodrigues Consuelo Junqueira , Chudzinski-Tavassi Ana Marisa
Published: June 2012

Lipocalin family members have been implicated in development, regeneration, and pathological processes, but their roles are unclear. Interestingly, these proteins are found abundant in the venom of theLonomia obliquacaterpillar. Lipocalins areβ-barrel proteins, which have three conserved motifs in their amino acid sequence. One of these motifs was shown to be a sequence signature involved in cell modulation. The aim of this study is to investigate the effects of a synthetic peptide comprising the lipocalin sequence motif in fibroblasts. This peptide suppressed caspase 3 activity and upregulated Bcl-2 and Ki-67, but did not interfere with GPCR calcium mobilization. Fibroblast responses also involved increased expression of proinflammatory mediators. Increase of extracellular matrix proteins, such as collagen, fibronectin, and tenascin, was observed. Increase in collagen content was also observed in vivo. Results indicate that modulation effects displayed by lipocalins through this sequence motif involve cell survival, extracellular matrix remodeling, and cytokine signaling. Such effects can be related to the lipocalin roles in disease, development, and tissue repair.
Physiologically Based Pharmacokinetic (PBPK) Modeling of Metabolic Pathways of Bromochloromethane in Rats
Authors: Cuello W. S. , Janes T. A. T. , Jessee J. M. , Venecek M. A. , Sawyer M. E. , Eklund C. R. , Evans M. V.
Published: June 2012

Bromochloromethane (BCM) is a volatile compound and a by-product of disinfection of water by chlorination. Physiologically based pharmacokinetic (PBPK) models are used in risk assessment applications. An updated PBPK model for BCM is generated and applied to hypotheses testing calibrated using vapor uptake data. The two different metabolic hypotheses examined are (1) a two-pathway model using both CYP2E1 and glutathione transferase enzymes and (2) a two-binding site model where metabolism can occur on one enzyme, CYP2E1. Our computer simulations show that both hypotheses describe the experimental data in a similar manner. The two pathway results were comparable to previously reported values (Vmax=3.8 mg/hour,Km=0.35 mg/liter, andkGST=4.7 /hour). The two binding site results wereVmax⁡1=3.7 mg/hour,Km⁡1=0.3 mg/hour, CL2= 0.047 liter/hour. In addition, we explore the sensitivity of different parameters for each model using our obtained optimized values.
Paradoxical Immune Reconstitution Syndrome Presenting as Acute Respiratory Distress Syndrome in a Leukemia Patient during Neutrophil Recovery
Authors: Alawin Issam A. , Karnath Bernard M.
Published: June 2012

Immune reconstitution inflammatory syndrome (IRIS) in the setting of antiretroviral therapy is well described, but it is not as common in non-HIV patients; here, we present a case of immune reconstitution inflammatory syndrome presenting as acute respiratory distress syndrome in a leukemia patient who had neutropenic fever and septic shock after high-dose cytarabine. During neutropenia recovery, his chest X-ray showed progressive worsening despite being on adequate therapy, we started him on steroids which resulted in significant clinical improvement.
Prognostic and Survival Factors in Myxofibrosarcomas
Authors: Dewan Varun , Darbyshire Anna , Sumathi Vaiyapuri , Jeys Lee , Grimer Robert
Published: June 2012

Aim. Our study aimed to determine prognostic factors for survival and recurrence in myxofibrosarcomas based on the experience of a single institution.Methods. Patients who had been diagnosed with a myxofibrosarcoma were identified from our database. Survival and recurrence were evaluated with Kaplan Meier survival curves for univariate and cox regression for multivariate analysis.Results. 174 patients with a diagnosis of myxofibrosarcoma were identified. Two patients were excluded due to incomplete information, leaving 172 patients with a mean age of 67 years. Surgery was undertaken in all but 6 patients. Five-year survival was better for myxofibrosarcomas when compared to other soft tissue sarcomas (63% versus 57%). Size, grade of tumour, age, and metastases were all found to be prognostic factors. Local recurrence occurred in 29 patients (17%) with an overall risk of 15% at 5 years. Previous inadvertent excision significantly raised this risk to 45%. Wide surgical margins and depth of tumour, however, had no impact on recurrence.Conclusion. Factors previously identified as prognostic did not demonstrate such a relationship in our study, highlighting the unpredictable nature of myxofibrosarcomas. Future treatment may lie in developing an understanding molecular basis of the tumour and directing therapies accordingly.
The Role of Fragile Sites in Sporadic Papillary Thyroid Carcinoma
Authors: Dillon Laura W. , Lehman Christine E. , Wang Yuh-Hwa
Published: June 2012

The incidence of thyroid cancer is increasing, especially papillary thyroid carcinoma (PTC), making it currently the fastest-growing cancer among women. Reasons for this increase remain unclear, but several risk factors including radiation exposure and improved detection techniques have been suggested. Recently, the induction of chromosomal fragile site breakage was found to result in the formation ofRET/PTC1rearrangements, a common cause of PTC. Chromosomal fragile sites are regions of the genome with a high susceptibility to forming DNA breaks and are often associated with cancer. Exposure to a variety of external agents can induce fragile site breakage, which may account for some of the observed increase in PTC. This paper discusses the role of fragile site breakage in PTC development, external fragile site-inducing agents that may be potential risk factors for PTC, and how these factors are especially targeting women.
Exposure to Nicotine and Carcinogens among Southwestern Alaskan Native Cigarette Smokers and Smokeless Tobacco Users
Authors: Benowitz Neal L. , Renner Caroline C. , Lanier Anne P. , Tyndale Rachel F. , Hatsukami Dorothy K. , Lindgren Bruce , Stepanov Irina , Watson Clifford H. , Sosnoff Connie S. , Jacob Peyton
Published: June 2012

Background: The prevalence of tobacco use, both cigarette smoking and smokeless, including iqmik (homemade smokeless tobacco prepared with dried tobacco leaves mixed with alkaline ash), and of tobacco-related cancer is high in Alaskan Native people (AN). To investigate possible mechanisms of increased cancer risk we studied levels of nicotine and tobacco-specific nitrosamines (TSNA) in tobacco products and biomarkers of tobacco toxicant exposure in Southwestern AN people.

Methods: Participants included 163 cigarette smokers, 76 commercial smokeless tobacco, 20 iqmik, 31 dual cigarette smokers and smokeless tobacco, and 110 nontobacco users. Tobacco use history, samples of tobacco products used, and blood and urine samples were collected.

Results: Nicotine concentrations were highest in cigarette tobacco and TSNAs highest in commercial smokeless tobacco products. The AN participants smoked on average 7.8 cigarettes per day. Nicotine exposure, assessed by several biomarker measures, was highest in iqmik users, and similar in smokeless tobacco and cigarette smokers. TSNA exposure was highest in smokeless tobacco users, and polycyclic aromatic hydrocarbon exposure was highest in cigarette smokers.

Conclusions: Despite smoking fewer cigarettes per day, AN cigarette smokers had similar daily intake of nicotine compared to the general U.S. population. Nicotine exposure was greatest from iqmik, likely related to its high pH due to preparation with ash, suggesting high addiction potential compared to other smokeless tobacco products. TSNA exposure was much higher with smokeless tobacco than other product use, possibly contributing to the high rates of oral cancer.

Impact: Our data contribute to an understanding of the high addiction risk of iqmik use and of the cancer-causing potential of various forms of tobacco use among AN people. Cancer Epidemiol Biomarkers Prev; 21(6); 934–42. ©2012 AACR.
Increased Levels of Tetra-antennary N-Linked Glycan but Not Core Fucosylation Are Associated with Hepatocellular Carcinoma Tissue
Authors: Mehta Anand , Norton Pamela , Liang Hongyan , Comunale Mary Ann , Wang Mengjun , Rodemich-Betesh Lucy , Koszycki Alex , Noda Katsuhisa , Miyoshi Eiji , Block Timothy
Published: June 2012

Background: Alterations in glycosylation have long been associated with the development of cancer. In the case of primary hepatocellular carcinoma (HCC), one alteration that has often been associated is increased amounts of fucose attached to the N-glycans of serum proteins secreted by the liver.

Methods: In an effort to determine the origin of this increased fucosylation, we have conducted N-linked glycan analysis of HCC tissue, the surrounding nontumor tissue, and compared this to tissue from a nondiseased adult liver.

Results: Surprisingly, no difference in the level of fucosylation was observed from the three donor groups, suggesting that the increased levels of fucosylation observed in serum of those with HCC is not the result of increased synthesis of fucosylated proteins in the cancer tissue. On the other hand, increased levels of a tetra-antennary glycan were observed in the HCC tissue as compared with the surrounding tissue or to the nondiseased livers.

Conclusions: This represents, to our knowledge, one of the first reports associating increased levels of branching with the development of HCC.

Impact: The identification of increased levels of tetra-antennary glycan on liver tumor tissue, as opposed to adjacent or nondiseased tissue may lead to improved detection of HCC. Cancer Epidemiol Biomarkers Prev; 21(6); 925–33. ©2012 AACR.