bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent advances in understanding the role of diet and obesity in the development of colorectal cancer
Authors: Lund Elizabeth K. , Belshaw Nigel J. , Elliott Giles O. , Johnson Ian T.
Published: March 2011

Colorectal cancer (CRC) is a major cause of premature death in the UK and many developed countries. However, the risk of developing CRC is well recognised to be associated not only with diet but also with obesity and lack of exercise. While epidemiological evidence shows an association with factors such as high red meat intake and low intake of vegetables, fibre and fish, the mechanisms underlying these effects are only now being elucidated. CRC develops over many years and is typically characterised by an accumulation of mutations, which may arise as a consequence of inherited polymorphisms in key genes, but more commonly as a result of spontaneously arising mutations affecting genes controlling cell proliferation, differentiation, apoptosis and DNA repair. Epigenetic changes are observed throughout the progress from normal morphology through formation of adenoma, and the subsequent development of carcinoma. The reasons why this accumulation of loss of homoeostatic controls arises are unclear but chronic inflammation has been proposed to play a central role. Obesity is associated with increased plasma levels of chemokines and adipokines characteristic of chronic systemic inflammation, and dietary factors such as fish oils and phytochemicals have been shown to have anti-inflammatory properties as well as modulating established risk factors such as apoptosis and cell proliferation. There is also some evidence that diet can modify epigenetic changes. This paper briefly reviews the current state of knowledge in relation to CRC development and considers evidence for potential mechanisms by which diet may modify risk.
Fruit of a contrasting colour is more detectable by frugivores
Authors: Melo Geruza Leal , Penatti Natasha Costa , Raizer Josué
Published: March 2011

Determination of the factors that rule the preference of birds for certain fruits is fundamental to the understanding of the co-evolution of plants and their dispersers (Alves-Costa & Lopes 2001). Plants might compete for dispersers, and the response of dispersers will differ according to the variety of fruits available in nature (Denslow & Moermond 1982, Herrera 1981). Seed dispersal by birds is directly related to certain features of fruit, including colour, size, shape, abundance, nutritional value, habitat and distance between plants that are fruiting (Alves-Costa & Lopes 2001, Galettiet al. 2003, Leveyet al. 1994, Murrayet al. 1993). To understand how birds integrate these features in terms of fruit choice is a complex and widely misunderstood problem (Leveyet al. 1994).
A Graph-Grabbing Game
Authors: MICEK PIOTR , WALCZAK BARTOSZ
Published: March 2011

Two players share a connected graph with non-negative weights on the vertices. They alternately take the vertices (one in each turn) and collect their weights. The rule they have to obey is that the remaining part of the graph must be connected after each move. We conjecture that the first player can get at least half of the weight of any tree with an even number of vertices. We provide a strategy for the first player to get at least 1/4 of an even tree. Moreover, we confirm the conjecture for subdivided stars. The parity condition is necessary: Alice gets nothing on a three-vertex path with all the weight at the middle. We suspect a kind of general parity phenomenon, namely, that the first player can gather a substantial portion of the weight of any ‘simple enough’ graph with an even number of vertices.
Poor post-operative growth in infants with two-ventricle physiology
Authors: Anderson Jeffrey B. , Marino Bradley S. , Irving Sharon Y. , García-España J. Felipe , Ravishankar Chitra , Stallings Virginia A. , Medoff-Cooper Barbara
Published: March 2011

Background

Adequate nutritional support is essential for normal infant growth and development. Infants with congenital cardiac disease are known to be at risk for growth failure. We sought to describe perioperative growth in infants undergoing surgical repair of two-ventricle congenital cardiac disease and assess for predictors of their pattern of growth.

Materials and methods

Full-term infants who underwent surgical repair of two-ventricle congenital cardiac disease at a single institution were enrolled in a retrospective cohort study performed following a larger prospective study. Infants with facial, gastrointestinal, or neurologic anomalies, trisomy chromosomal abnormality, birth weight less than 2500 grams, or those transferred to another institution before discharge home were excluded. The primary outcome was change in weight-for-age z score from surgery to discharge. Our secondary outcome variable was post-operative hospital length of stay.

Results

A total of 76 infants met the inclusion criteria. Medain age at surgery was 5 days with a range from 1 to 44. The median weight-for-age z score at surgery was −0.2 with a range from −2.9 to 2.8 and by discharge had dropped to −1.2 with a range from −3.4 to 1.8. The median change in weight-for-age z score from surgery to discharge was −1.0 with a range from −2.3 to 0.2. Delayed post-operative nutrition (p < 0.001) and reintubation following initial post-operative extubation (p = 0.001) were associated with decrease in weight-for-age z score.

Conclusions

Infants undergoing repair of two-ventricle congenital cardiac disease had poor growth in the post-operative period. This may be mitigated by early initiation of post-operative nutrition.
Reduced Cognitive Control of a Visually Bistable Image in Schizophrenia
Authors: McBain Ryan , Norton Daniel J. , Kim Jejoong , Chen Yue
Published: March 2011

Schizophrenia is associated with the inability to control and coordinate thoughts, actions, and perceptions. In conventional assessments of cognitive control, multiple sensory features of stimuli are concomitantly manipulated, introducing a confounding role of bottom-up perceptual information. To overcome this difficulty, we used an ambiguous visual stimulus (Necker cube), which allowed measurement of cognitive control with constant sensory input. Subjects (20 patients, 20 controls) were asked to control their perception of a transparent Necker cube by keeping a designated plane at the front or back of the stimulus, the position of which is perceptually bistable. Patients were highly deficient at controlling their perception of the cube. When a visual feature (the luminance contrast between a designated cube plane and the other planes) was systematically manipulated, an interaction was found whereby schizophrenia patients no longer under-performed on the highest contrast condition. These results show patients’ impairment of controlling perception in the absence of visual modulation and suggest the potential utility of perceptually based approaches to cognitive remediation in schizophrenia. (JINS, 2011, 551–556)
Live, Video-Rate Super-Resolution Microscopy Using Structured Illumination and Rapid GPU-Based Parallel Processing
Authors: Lefman Jonathan , Scott Keana , Stranick Stephan
Published: March 2011

Structured illumination fluorescence microscopy is a powerful super-resolution method that is capable of achieving a resolution below 100 nm. Each super-resolution image is computationally constructed from a set of differentially illuminated images. However, real-time application of structured illumination microscopy (SIM) has generally been limited due to the computational overhead needed to generate super-resolution images. Here, we have developed a real-time SIM system that incorporates graphic processing unit (GPU) based in-line parallel processing of raw/differentially illuminated images. By using GPU processing, the system has achieved a 90-fold increase in processing speed compared to performing equivalent operations on a multiprocessor computer—the total throughput of the system is limited by data acquisition speed, but not by image processing. Overall, more than 350 raw images (16-bit depth, 512 × 512 pixels) can be processed per second, resulting in a maximum frame rate of 39 super-resolution images per second. This ultrafast processing capability is used to provide immediate feedback of super-resolution images for real-time display. These developments are increasing the potential for sophisticated super-resolution imaging applications.
The Historic Records of the Judicial Function of the UK Parliament
Authors: Shenton Caroline
Published: March 2011

This article by Caroline Shenton, Clerk of the Records at the Parliamentary Archives, describes the rich legacy of records relating to the judicial function of the House of Lords from the sixteenth century to 2009, when the new Supreme Court was established.
Research and Resources for Corporate Lawyers
Authors: Breslin Jas
Published: March 2011

Jas Breslin gives a brief overview of the type of work corporate lawyers are involved with and the key resources that they need.
Seismic interpretation of pelagic sedimentation regimes in the 18–53 Ma eastern equatorial Pacific: Basin‐scale sedimentation and infilling of abyssal valleys
Authors: Tominaga Masako , Lyle Mitchell , Mitchell Neil C.
Published: March 2011

Understanding how pelagic sediment has been eroded, transported, and deposited is critical to evaluating pelagic sediment records for paleoceanography. We use digital seismic reflection data from an Integrated Ocean Drilling Program site survey (AMAT03) to investigate pelagic sedimentation across the eastern‐central equatorial Pacific, which represents the first comprehensive record published covering the 18–53 Ma eastern equatorial Pacific. Our goals are to quantify (1) basin‐hill‐scale primary deposition regimes and (2) the extent to which seafloor topography has been subdued by abyssal valley‐filling sediments. The eastern Pacific seafloor consists of a series of abyssal hills and basins, with minor late stage faulting in the basement. Ocean crust rarely outcrops at the seafloor away from the rise crest; both hills and basins are sediment covered. The carbonate compensation depth is identified at 4440 m by the appearance of acoustically transparent clay intervals in the seismic data. Overall, we recognized three different sedimentation regimes: depositional (high sedimentation rate), transitional, and minimal sedimentation (low sedimentation rate) regimes. In all areas, the sedimented seafloor mimics the underlying basement topography, although the degree to which topography becomes subdued varies. Depositional regimes result in symmetric sedimentation within basins and subdued topography, whereas minimal sedimentation regimes have more asymmetric distribution of sediments within topographic lows and higher seafloor relief. Regardless of sedimentation regime, enhanced sediment deposition occurs within basins. However, we observe that basin infill is rarely more than twice as thick as sediment cover over abyssal hills. If this variation is due to sediment focusing, the focusing factor in the basins, as measured by 230Th, is no more than a factor of ∼1.3 of the total vertical particulate rain.
Probing the depths of the India‐Asia collision: U‐Th‐Pb monazite chronology of granulites from NW Bhutan
Authors: Warren C. J. , Grujic D. , Kellett D. A. , Cottle J. , Jamieson R. A. , Ghalley K. S.
Published: March 2011

Rocks metamorphosed to high temperatures and/or high pressures are rare across the Himalayan orogen, where peak metamorphic conditions recorded in the exposed metamorphic core, the Greater Himalayan Sequence (GHS), are generally at middle to upper amphibolite facies. However, mafic garnet‐clinopyroxene assemblages exposed at the highest structural levels in Bhutan, eastern Himalaya, preserve patchy textural evidence for early eclogite‐facies conditions, overprinted by granulite‐facies conditions. Monazite hosted within the leucosome of neighboring granulite‐facies orthopyroxene‐bearing felsic gneiss yields LA‐MC‐ICP‐MS U‐Th‐Pb ages of 13.9 ± 0.3 Ma. Monazite associated with sillimanite‐grade metamorphism in granulite‐hosting migmatitic gneisses yields U‐Th‐Pb rim ages between 15.4 ± 0.8 Ma and 13.4 ± 0.5 Ma. Monazite associated with sillimanite‐grade metamorphism in gneiss at structurally lower levels yields U‐Pb rim ages of 21–17 Ma. These data are consistent with Miocene exhumation of GHS material from a variety of crustal depths at different times along the Himalayan orogen. We propose that these granulitized eclogites represent lower crustal material exhumed by tectonic forcing over an incoming Indian crustal ramp and that they formed in a different tectonic regime to the ultrahigh‐pressure eclogites in the western Himalaya. Their formation and exhumation in the Miocene therefore do not require diachroneity in the timing of the initial India‐Asia collision.
Vascular phenotyping of brain tumors using magnetic resonance microscopy (μMRI)
Authors: Kim Eugene , Zhang Jiangyang , Hong Karen , Benoit Nicole E , Pathak Arvind P
Published: March 2011

Abnormal vascular phenotypes have been implicated in neuropathologies ranging from Alzheimer's disease to brain tumors. The development of transgenic mouse models of such diseases has created a crucial need for characterizing the murine neurovasculature. Although histologic techniques are excellent for imaging the microvasculature at submicron resolutions, they offer only limited coverage. It is also challenging to reconstruct the three-dimensional (3D) vasculature and other structures, such as white matter tracts, after tissue sectioning. Here, we describe a novel method for 3D whole-brain mapping of the murine vasculature using magnetic resonance microscopy (μMRI), and its application to a preclinical brain tumor model. The 3D vascular architecture was characterized by six morphologic parameters: vessel length, vessel radius, microvessel density, length per unit volume, fractional blood volume, and tortuosity. Region-of-interest analysis showed significant differences in the vascular phenotype between the tumor and the contralateral brain, as well as between postinoculation day 12 and day 17 tumors. These results unequivocally show the feasibility of using μMRI to characterize the vascular phenotype of brain tumors. Finally, we show that combining these vascular data with coregistered images acquired with diffusion-weighted MRI provides a new tool for investigating the relationship between angiogenesis and concomitant changes in the brain tumor microenvironment.
Antiplatelet Pretreatment does not Increase Hematoma Volume in Experimental Intracerebral Hemorrhage
Authors: Lauer Arne , Schlunk Frieder , Van Cott Elizabeth M , Steinmetz Helmuth , Lo Eng H , Foerch Christian
Published: March 2011

While oral anticoagulants are associated with greater hematoma expansion and higher mortality rates in patients with intracerebral hemorrhage (ICH), there is ongoing discussion whether pretreatment with antiplatelet drugs also worsens prognosis. Using an experimental model of ICH, we investigated the effects of antiplatelet pretreatment on hematoma volume and functional outcome. CD-1 mice were treated with acetyl-salicylic acid (ASA, 60 mg/kg per 24 hours), clopidogrel (22.5 mg/kg per 24 hours), or both (ASA + clopidogrel) through drinking water for 3 days ( n = 20 per group). Thereafter, platelet aggregation was found to be significantly reduced. Untreated mice and mice pretreated with warfarin served as controls. A stereotactic injection of collagenase into the right striatum was used to induce ICH. Twenty-four hours after ICH induction, hematoma volume was measured to be 15.0 ± 4.4 µL in controls, 14.1 ± 5.3 µL in ASA mice, 16.8 ± 5.1 µL in clopidogrel mice, and 16.4 ± 5.1 µL in ASA + clopidogrel animals. These differences were not statistically significant. However, mice pretreated with warfarin revealed largely increased hematoma volumes (25.0 ± 7.4 µL versus controls, P = 0.001). Neurologic outcome was not different between antiplatelet-pretreated animals and untreated controls. Our results suggest that plasmatic coagulation rather than platelet function is the most critical element for preventing hematoma expansion in acute ICH. Future therapeutic strategies may take these findings into account.
Contributions of Morphological Awareness Skills to Word-Level Reading and Spelling in First-Grade Children With and Without Speech Sound Disorder
Authors: Apel Kenn , Lawrence Jessika
Published: March 2011

Purpose

In this study, the authors compared the morphological awareness abilities of children with speech sound disorder (SSD) and children with typical speech skills and examined how morphological awareness ability predicted word-level reading and spelling performance above other known contributors to literacy development.

Method

Eighty-eight first-grade students—44 students with SSD and no known history of language deficiencies, and 44 students with typical speech and language skills—completed an assessment battery designed to measure speech sound production, morphological awareness, phonemic awareness, letter-name knowledge, receptive vocabulary, word-level reading, and spelling abilities.

Results

The children with SSD scored significantly lower than did their counterparts on the morphological awareness measures as well as on phonemic awareness, word-level reading, and spelling tasks. Regression analyses suggested that morphological awareness predicted significant unique variance on the spelling measure for both groups and on the word-level reading measure for the children with typical skills.

Conclusion

These results suggest that children with SSD may present with a general linguistic awareness insufficiency, which puts them at risk for difficulties with literacy and literacy-related tasks.
Modeling and simulation of heterojunction crystalline silicon solar cells with a nanocrystalline cubic silicon carbide emitter
Authors: Miyajima Shinsuke , Irikawa Junpei , Yamada Akira , Konagai Makoto
Published: March 2011

We have developed a simulation model for a heterojunction crystalline silicon (HJ-c-Si) solar cell with an n-type hydrogenated nanocrystalline cubic silicon carbide (nc-3C-SiC:H) emitter and a p-type hydrogenated microcrystalline silicon oxide back surface field layer. Analyses of experimentally obtained solar-cell performance using the simulation model indicate that the conversion efficiency of the solar cell is limited by the rear-surface recombination velocity (Sr) and acceptor concentration (NA) of the p-type c-Si base region. Simulation results indicate that a potential conversion efficiency of HJ-c-Si solar cells using n-type nc-3C-SiC:H emitters is approximately 23% when Sr, NA, and bulk lifetime of the p-type base are 10 cm/s, 2 × 1016 cm−3, and 1.0 × 10−3 s, respectively.
Time-dependent degradation of Pt/ZnO nanoneedle rectifying contact based piezoelectric nanogenerator
Authors: Periasamy C. , Chakrabarti P.
Published: March 2011

A piezoelectric nanogenerator based on the platinum rectifying contact on ZnO nanoneedle arrays (NNA) has been successfully fabricated on silicon substrate by using the thermal evaporation deposition technique. It is demonstrated that the rectifying platinum contact on ZnO NNA can efficiently convert nanoscale mechanical energy into electrical energy by exploiting the piezoelectric and semiconducting properties of ZnO. The effect of key parameters such as scanning speed, force on scanning tip, and tip abrasion on the nanogenerator has been studied along with long-time stability of the piezoelectric nanogenerator. The study reveals that the nanogenerator output degrades with time primarily due to degradation of the rectifying contact with time and abrasion of the tip caused by repeated scanning. The results of the study are expected to provide quantitative ideas about the long-time stability of ZnO NN based nanogenerators.
Dynamics of C2 formation in laser-produced carbon plasma in helium environment
Authors: Al-Shboul K. F. , Harilal S. S. , Hassanein A. , Polek M.
Published: March 2011

We investigated the role of helium ambient gas on the dynamics of C2 species formation in laser-produced carbon plasma. The plasma was produced by focusing 1064 nm pulses from an Nd:YAG laser onto a carbon target. The emission from the C2 species was studied using optical emission spectroscopy, and spectrally resolved and integrated fast imaging. Our results indicate that the formation of C2 in the plasma plume is strongly affected by the pressure of the He gas. In vacuum, the C2 emission zone was located near the target and C2 intensity oscillations were observed both in axial and radial directions with increasing the He pressure. The oscillations in C2 intensity at higher pressures in the expanding plume could be caused by various formation zones of carbon dimers.
The elusive half-pole in the frequency domain transfer function of Peltier thermoelectric devices
Authors: De Marchi Andrea , Giaretto Valter
Published: March 2011

A half-pole can be expected in the transfer function of a Peltier device because proportionality between the diffusion length and the square root of the diffusion time is intrinsic in the diffusion equation. The resulting −1/2 bilogarithmic slope (10 dB/dec) is, however, easily masked by the thermal time constant of the load, which makes it elusive. The goal of this work is to identify the arrangements which can reveal and make usable the half-pole, because the latter can be instrumental in a servo control to increase the open-loop gain without risking instability. The diffusion equation was solved in a sine wave regime for a one-dimensional model of a Peltier device. The Laplace transform method was used, and the periodic solution was obtained using Cauchy's theorem and the method of residues. The −1/2 slope of the half-pole appeared observable in a frequency range which can be several decades wide, depending on details of device configuration and considered position within. Amplitude and phase of temperature and heat flux in various spots are discussed with emphasis on the physical meaning, and a comparison is provided with solutions yielded by the lumped model, which cannot show the half-pole. An experimental check of the theoretical approach and analysis was made taking into account the deviations from one-dimensionality occurring in a real Peltier device. Given a constant amplitude sine wave injected current, the quadrature component of the Seebeck voltage across the whole series of junctions was identified as the most easily measurable quantity related to the thermal response of the device. Experimental results for the latter turned out in good agreement with analytical solutions.
Resonant ultrasound spectroscopy of cylinders over the full range of Poisson's ratio
Authors: Jaglinski Tim , Lakes Roderic S.
Published: March 2011

Mode structure maps for freely vibrating cylinders over a range of Poisson's ratio, ν, are desirable for the design and interpretation of experiments using resonant ultrasound spectroscopy (RUS). The full range of isotropic ν (–1 to +0.5) is analyzed here using a finite element method to accommodate materials with a negative Poisson's ratio. The fundamental torsional mode has the lowest frequency provided ν is between about –0.24 and +0.5. For any ν, the torsional mode can be identified utilizing the polarization sensitivity of the shear transducers. RUS experimental results for materials with Poisson's ratio +0.3, +0.16, and –0.3 and a previous numerical study for ν = 0.33 are compared with the present analysis. Interpretation of results is easiest if the length/diameter ratio of the cylinder is close to 1. Slight material anisotropy leads to splitting of the higher modes but not of the fundamental torsion mode.
Nitrogen, phosphorus, and potassium prediction in soils, using infrared spectroscopy
Authors: Shao Yongni , He Yong
Published: March 2011

The aim of this study was to investigate the potential of the infrared spectroscopy technique for non-destructive measurement of soil properties. For the study, 280 soil samples were collected from several regions in Zhejiang, China. Data from near infrared (NIR, 800–2500 nm), mid infrared (MIR, 4000–400 cm–1), and the combined NIR–MIR regions were compared to determine which produced the best prediction of soil properties. Least-squares support vector machines (LS-SVM) were applied to construct calibration models for soil properties such as available nitrogen (N), phosphorus (P), and potassium (K). The results showed that both spectral regions contained substantial information on N, P, and K in the soils studied, and the combined NIR–MIR region did a little worse than either the NIR or MIR region. Optimal results were obtained through LS-SVM compared with the standard partial least-squares regression method, and the correlation coefficient of prediction (rp), root mean square error for prediction, and bias were, respectively, 0.90, 16.28 mg/kg, and 0.96 mg/kg for the prediction results of N in the NIR region; and 0.88, 41.62 mg/kg, and –2.28 mg/kg for the prediction results of P, and 0.89, 33.47 mg/kg, and 2.96 mg/kg for the prediction results of K, both in the MIR region. This work demonstrated the potential of LS-SVM coupled to infrared reflectance spectroscopy for more efficient soil analysis and the acquisition of soil information.
Transcriptional and posttranslational up-regulation of HER3 (ErbB3) compensates for inhibition of the HER2 tyrosine kinase
Authors: Garrett Joan T. , Olivares María Graciela , Rinehart Cammie , Granja-Ingram Nara D. , Sánchez Violeta , Chakrabarty Anindita , Dave Bhuvanesh , Cook Rebecca S. , Pao William , McKinely Eliot , Manning H. C. , Chang Jenny , Arteaga Carlos L.
Published: March 2011

Sustained and complete inhibition of HER3 and its output to PI3K/Akt are required for the optimal antitumor effect of therapeutic inhibitors of the HER2 oncogene. Here, we show that, after inhibition of the HER2 tyrosine kinase with lapatinib, there is PI3K/Akt and FoxO3a-dependent up-regulation of HER3 mRNA and protein. Up-regulated HER3 was then phosphorylated by residual HER2 activity, thus partially maintaining P-Akt and limiting the antitumor action of lapatinib. Inhibition of HER3 with siRNA or a neutralizing HER3 antibody sensitized HER2+ breast cancer cells and xenografts to lapatinib both in vitro and in vivo. Combined blockade of HER2 and HER3 inhibited pharmacodynamic biomarkers of PI3K/Akt activity more effectively than each inhibitor alone. These results suggest that because of HER3-mediated compensation, current clinical inhibitors of HER2 and PI3K/Akt will not block the PI3K pathway completely. They also suggest that therapeutic inhibitors of HER3 should be used in combination with HER2 inhibitors and PI3K pathway inhibitors in patients with HER2- and PI3K-dependent cancers.
Temporal trends and spatial patterns in the temperature and oxygen regimes in the Bay of Quinte, Lake Ontario, 1972–2008
Authors: Minns Charles K. , Moore James E. , Doka Susan E. , St. John Margaretha A.
Published: March 2011

The temperature and oxygen regimes of the Bay of Quinte have been monitored, weekly or biweekly, in the open water season at a series of offshore index sites since 1972. Since 2001, temperature has been monitored in situ using loggers at both offshore and nearshore sites. This study was undertaken to assess the potential role of morphometry, climate, nutrient loading, and invasion by dreissenids in temporal trends and spatial patterns of temperature and oxygen regimes. The thermal regime was assessed using summer surface temperatures, Schmidt's vertical stability values, and vertical stratification characteristics. When the Quinte studies began taking measurements in the hypolimnion, deeper stations were attaining low oxygen levels by the end of summer, raising concerns that the cumulative impacts of eutrophication might lead to anoxia. The bottom oxygen regime at sites that stratified was assessed using the hypolimnetic warming rates and the apparent oxygen depletion rates one meter off the bottom. Quinte's maximum summer surface waters have warmed almost 1oC from 1972 to 2008 in line with climate warming. Nearshore sites in the shallow upper Bay have similar temperatures to offshore index sites while those in the lower Bay are warmer. The warming of surface waters has increased the maximum Schmidt's stability values at the deeper sites but thermocline depth or bottom temperatures have not changed. Hypolimnetic warming rates showed no temporal change but were inversely correlated with mean summer flow from the main river draining into the Bay. Oxygen depletion was variable but exhibited a downward trend in response to reduced phosphorus loading with neither climate warming nor the driessenid invasion having a detectable effect. Projected 21st C climate warming poses a threat to the Bay of Quinte ecosystem.
Applying a regional coastal wetland monitoring framework to refine and report on wildlife and habitat delisting criteria in the Bay of Quinte Area of Concern
Authors: Macecek Diana , Grabas Greg P.
Published: March 2011

In most Canadian Areas of Concern, fish and wildlife populations and their habitats (i.e. Beneficial Use Impairments 3 and 14) have been listed as impaired. While much work has addressed other Beneficial Use Impairments, there has often been a lack of specific data and methodologies for evaluating fish and wildlife populations and their habitats. This article presents a methodology for refining delisting criteria for wildlife and habitat Beneficial Use Impairments in the Bay of Quinte Area of Concern using indices of condition in a coastal wetland monitoring framework. Data have been collected to provide information on loss of fish and wildlife habitat (water quality and submerged aquatic vegetation and aquatic macroinvertebrate communities) and degradation of fish and wildlife populations (fish, amphibian and breeding bird communities). Three potential models for delisting are presented using the submerged aquatic vegetation community data as an example. For all coastal wetland attributes considered through the framework, Bay of Quinte coastal wetlands were generally in better condition than other Canadian sites along the Lake Ontario shoreline.
Changes in zooplankton biomass in the Bay of Quinte with the arrival of the mussels, Dreissena polymorpha and D. rostiformis bugensis, and the predatory cladoceran, Cercopagis pengoi: 1975 to 2008
Authors: Bowen Kelly L. , Johannsson Ora E.
Published: March 2011

Long term monitoring of Lake Ontario's Bay of Quinte provides the opportunity to examine the impact of dreissenid invasion on the zooplankton community. Weekly or biweekly zooplankton samples have been collected from 1975 to 2008 at 3 stations: Belleville (B), Hay Bay (HB), and Conway (C) along a trophic and depth gradient down the bay. Rotifers have been collected since 2000. Biomass estimates based on measured zooplankton lengths started in 1995. Archived seasonal composite samples prior to 1995 were reanalysed and biomass recalculated from length-weight equations to allow for comparable data in trend analysis. Mean May 1– October 6 zooplankton biomass was low from 1975 into the early 1980s and peaked between 1982–1983 and 1991. Biomass fell during the cold summer of 1992 associated with the Pinatubo eruption and was low after the invasion of dreissenid mussels. From 1979–1991 (after phosphorus control and prior to dreissenid invasion), biomass averaged 265, 253 and 84 mg m−3 at B, HB and C, respectively. Seasonal biomass of most zooplankton groups, as well as total biomass, was significantly lower at all stations after the dreissenid invasion. Cladocerans still dominated zooplankton biomass after the invasion, averaging 56% to 80% of the total. Cyclopoid numbers and biomass fell dramatically.

After the invasion of  Cercopagis pengoi in 1999, calanoid and cyclopoid biomass at HB and C decreased by approximately 50%. Bosmina biomass did not change. Seasonal mean rotifer biomass over the 2000 to 2008 period was 1.9% to 4.4% of total zooplankton biomass.

Reductions in zooplankton following dreissenid and C. pengoi invasions are thought to be caused by both direct predation of microzooplankton (e.g. nauplii) by mussels and copepods by C. pengoi (at C and HB), and competition between zooplankton and dreissenids for food resources.
The phytoplankton of the Bay of Quinte, 1972–2008: point-source phosphorus loading control, dreissenid mussel establishment, and a proposed community reference
Authors: Nicholls Kenneth H. , Carney Elaine C.
Published: March 2011

The objective of this contribution is to further the understanding of long-term (37 years) changes in the composition and biomass of the phytoplankton of the Bay of Quinte (northeastern Lake Ontario), especially those changes associated with the simultaneous point-source phosphorus loading reduction/white perch winter kill of early 1978 and the establishment of dreissenid mussels in the mid-1990’s. The relatively shallow and polymictic upper bay has facilitated the ice-free period domination of the phytoplankton by meroplanktonic diatoms (especially Aulacoseira spp.); while a more balanced representation by several algal Divisions has characterized the thermally stratified, dimictic lower bay. At all three stations (upper bay, middle bay and lower bay), phytoplankton biomass declined and community similarity decreased after both the phosphorus loading and the Dreissena interventions, but the biomass changes associated with the P load reduction were greater than those associated with Dreissena establishment. Conversely, the loss of phytoplankton community similarity after Dreissena establishment was greater than that associated with P loading reduction at all three stations. The Remedial Action Plan phytoplankton objective of 4–5 mm3 l−1 (May-October mean) has been met inconsistently since the establishment of Dreissena. The post-Dreissena period, however, was also characterized by occasional very high biomass values for the potentially toxic cyanoprokaryote (blue-green alga) Microcystis, as well as by a dramatic decline in the bloom-forming blue-green Aphanizomenon, and the near extirpation of the diatoms, Tabellaria and Synedra spp. A partially synthetic phytoplankton community was constructed using data taken from three local aquatic systems (Trenton Bay, upper Hay Bay and West Lake). This might be used as a reference against which past and future changes in the upper Bay of Quinte phytoplankton can be compared and evaluated.
Magnetic flux density reconstruction using interleaved partial Fourier acquisitions in MREIT
Authors: Park Hee Myung , Nam Hyun Soo , Kwon Oh In
Published: March 2011

Magnetic resonance electrical impedance tomography (MREIT) has been introduced as a non-invasive modality to visualize the internal conductivity and/or current density of an electrically conductive object by the injection of current. In order to measure a magnetic flux density signal in MREIT, the phase difference approach in an interleaved encoding scheme cancels the systematic artifacts accumulated in phase signals and also reduces the random noise effect. However, it is important to reduce scan duration maintaining spatial resolution and sufficient contrast, in order to allow for practical in vivo implementation of MREIT. The purpose of this paper is to develop a coupled partial Fourier strategy in the interleaved sampling in order to reduce the total imaging time for an MREIT acquisition, whilst maintaining an SNR of the measured magnetic flux density comparable to what is achieved with complete k-space data. The proposed method uses two key steps: one is to update the magnetic flux density by updating the complex densities using the partially interleaved k-space data and the other is to fill in the missing k-space data iteratively using the updated background field inhomogeneity and magnetic flux density data. Results from numerical simulations and animal experiments demonstrate that the proposed method reduces considerably the scanning time and provides resolution of the recovered Bz
comparable to what is obtained from complete k-space data.
Numerical Validation and Comparison of Three Solar Wind Heating Methods by the SIP-CESE MHD Model
Authors: Yang Li-Ping , Feng Xue-Shang , Xiang Chang-Qing , Jiang Chao-Wei
Published: March 2011

We conduct simulations using the three-dimensional (3D) solar-interplanetary conservation element/solution element (SIP-CESE) magnetohydrodynamic (MHD) model and magnetogram data from a Carrington rotation (CR) 1897 to compare the three commonly used heating methods, i.e. the Wentzel—Kramers—Brillouin (WKB) Alfvén wave heating method, the turbulence heating method and the volumetric heating method. Our results show that all three heating models can basically reproduce the bimodal structure of the solar wind observed near the solar minimum. The results also demonstrate that the major acceleration interval terminates about 4RSfor the turbulence heating method and 10RSfor both the WKB Alfvén wave heating method and the volumetric heating method. The turbulence heating and the volumetric heating methods can capture the observed changing trends by the WIND satellite, while the WKB Alfvén wave heating method does not.
Nanosized perovskite oxide NdFeO
3 as material for a carbon-monoxide catalytic gas sensor
Authors: Ho Truong Giang , Ha Thai Duy , Pham Quang Ngan , Giang Hong Thai , Thu Do Thi Anh , Nguyen Ngoc Toan
Published: March 2011

In this paper, research on a CO catalytic gas sensor based on nano-crystalline perovskite oxide NdFeO
3 designed for exhaust gas measurement is presented. Nano-crystalline oxide NdFeO
3 was synthesized by a sol–gel citrate technique. The gas sensing characteristics of this sensor were investigated in the concentration range of CO between 0 and 5 vol.% in air. The influences of C
3
H
8, C
4
H
16 gases, relative humidity and air-flow rate on the cross-sensitivity of the CO sensor were also studied.
A micro-extractor for concentration and determination of lead in water
Authors: Van Man Tran , Berthier Jean , Ozil Patrick , Sarrut Nicolas
Published: March 2011

In this work, we present the design, fabrication and characterization of a novel micro-extractor that performs on-line extraction–concentration–detection (ECD) of target molecules flowing in a carrier liquid. The system comprises a primary microchannel containing a flowing aqueous carrier liquid and a secondary organic storage fluid circulating in an adjacent channel. The interfaces between the two immiscible fluids are stabilized by vertical micro-pillars. The system encompasses three functions: (i) extraction of the target molecules from the carrier fluid through the pillar-stabilized interfaces, (ii) concentration of the targets in the secondary organic solvent due to its very low—or zero—velocity and (iii) on-line detection via optical spectrometry. We successively present the analysis of the physics of the system, which has led us to a specific design, then the microfabrication of the chip, and finally we demonstrate the extraction, concentration and detection of lead ions (Pb
2+) from a water flow.
𝒞⁰ penalty methods for the fully nonlinear Monge-Ampère equation
Authors: Brenner Susanne , Gudi Thirupathi , Neilan Michael , Sung Li-yeng
Published: March 2011

In this paper, we develop and analyze

C

0

\mathcal {C}^0

penalty methods for the fully nonlinear Monge-Ampère equation

det
(

D
2

u
)
=
f

\det (D^2 u) = f

in two dimensions. The key idea in designing our methods is to build discretizations such that the resulting discrete linearizations are symmetric, stable, and consistent with the continuous linearization. We are then able to show the well-posedness of the penalty method as well as quasi-optimal error estimates using the Banach fixed-point theorem as our main tool. Numerical experiments are presented which support the theoretical results.
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data
Authors: Jefferys Stuart R. , Giddings Morgan C.
Published: March 2011

Motivation: Post-translational modifications are vital to the function of proteins, but are hard to study, especially since several modified isoforms of a protein may be present simultaneously. Mass spectrometers are a great tool for investigating modified proteins, but the data they provide is often incomplete, ambiguous and difficult to interpret. Combining data from multiple experimental techniques—especially bottom-up and top-down mass spectrometry—provides complementary information. When integrated with background knowledge this allows a human expert to interpret what modifications are present and where on a protein they are located. However, the process is arduous and for high-throughput applications needs to be automated.

Results: This article explores a data integration methodology based on Markov chain Monte Carlo and simulated annealing. Our software, the Protein Inference Engine (the PIE) applies these algorithms using a modular approach, allowing multiple types of data to be considered simultaneously and for new data types to be added as needed. Even for complicated data representing multiple modifications and several isoforms, the PIE generates accurate modification predictions, including location. When applied to experimental data collected on the L7/L12 ribosomal protein the PIE was able to make predictions consistent with manual interpretation for several different L7/L12 isoforms using a combination of bottom-up data with experimentally identified intact masses.

Availability: Software, demo projects and source can be downloaded from http://pie.giddingslab.org/

Contact:  morgan@giddingslab.org.

Supplementary information:  Supplementary data are available at Bioinformatics online
Peptide transport and animal growth: the fish paradigm
Authors: Verri Tiziano , Terova Genciana , Dabrowski Konrad , Saroglia Marco
Published: March 2011

Protein digestion products are transported from the intestinal lumen into the enterocyte both in the form of free amino acids (AAs), by a large variety of brush border membrane AA transporters, and in the form of di/tripeptides, by a single brush border membrane transporter known as PEPtide Transporter 1 (PEPT1). Recent data indicate that, at least in teleost fish, PEPT1 plays a significant role in animal growth by operating, at the gastrointestinal level, as part of an integrated response network to food availability that directly supports body weight. Notably, PEPT1 responds to both fasting and refeeding and is involved in a phenomenon known as compensatory growth (a phase of accelerated growth when food levels are restored after a period of growth depression). In particular, PEPT1 expression decreases during fasting and increases during refeeding, which is the opposite of what observed so far in mammals and birds. These findings in teleost fish document, to our knowledge, for the first time in a vertebrate model, a direct correlation between the expression of an intestinal transporter, such as PEPT1, primarily involved in the uptake of dietary protein degradation products and animal growth.
A first estimate of white shark,
Carcharodon carcharias
, abundance off Central California
Authors: Chapple Taylor K. , Jorgensen Salvador J. , Anderson Scot D. , Kanive Paul E. , Klimley A. Peter , Botsford Louis W. , Block Barbara A.
Published: March 2011

The decline of sharks in the global oceans underscores the need for careful assessment and monitoring of remaining populations. The northeastern Pacific is the home range for a genetically distinct clade of white sharks (
Carcharodon carcharias
). Little is known about the conservation status of this demographically isolated population, concentrated seasonally at two discrete aggregation sites: Central California (CCA) and Guadalupe Island, Mexico. We used photo-identification of dorsal fins in a sequential Bayesian mark–recapture algorithm to estimate white shark abundance off CCA. We collected 321 photographs identifying 130 unique individuals, and estimated the abundance off CCA to be 219 mature and sub-adult individuals ((130, 275) 95% credible intervals), substantially smaller than populations of other large marine predators. Our methods can be readily expanded to estimate shark population abundance at other locations, and over time, to monitor the status, population trends and protection needs of these globally distributed predators.
The influence of disorder on deformations in semiflexible networks
Authors: Blundell Jamie R. , Terentjev Eugene M.
Published: March 2011

We present a model that assesses the different elastic responses of a semiflexible network, which either (i) is constrained to deform in an affine way or (ii) is permitted to thermally fluctuate and deviate from affine response. The thermal, non-affine response of the network is achieved using a Metropolis Monte Carlo algorithm with dynamic step size. We find that non-affine deformations soften the network dramatically at low strains and make the eventual nonlinear strain stiffening far more pronounced. We show that the effect of these non-affine deformations are very sensitive to the degree variation in the lengths of filaments connecting cross-links. Where there is high variation, non-affine deformations allow internal stresses to relax, giving rise to a smaller range of tensile forces in filaments and a dramatic reduction of network stiffness. This highlights that non-affine deformations are crucial in small strain response of stiff polymer networks.
A study on the principle of maximum dissipation for coupled and non-coupled non-isothermal processes in materials
Authors: Hackl Klaus , Fischer Franz Dieter , Svoboda Jiri
Published: March 2011

The expression for entropy production owing to diffusion used in Hackl
et al.
(2010
Proc. R. Soc. A
467
, 1186–1196. (
doi:10.1098/rspa.2010.0179
)) has led to some discussion concerning its definition and comparability with terms found in the literature. Therefore, in this addendum, we introduce a slight modification which leads to a more consistent result that can be better interpreted in the light of existing literature.
Avian maternal response to chick distress
Authors: Edgar J. L. , Lowe J. C. , Paul E. S. , Nicol C. J.
Published: March 2011

The extent to which an animal is affected by the pain or distress of a conspecific will depend on its capacity for empathy. Empathy most probably evolved to facilitate parental care, so the current study assessed whether birds responded to an aversive stimulus directed at their chicks. Domestic hens were exposed to two replicates of the following conditions in a counterbalanced order: control (C; hen and chicks undisturbed), air puff to chicks (APC; air puff directed at chicks at 30 s intervals), air puff to hen (APH; air puff directed at hen at 30 s intervals) and control with noise (CN; noise of air puff at 30 s intervals). During each test, the hens' behaviour and physiology were measured throughout a 10 min pre-treatment and a 10 min treatment period. Hens responded to APH and APC treatments with increased alertness, decreased preening behaviour and a reduction in eye temperature. No such changes occurred during any control period. Increased heart rate and maternal vocalization occurred exclusively during the APC treatment, even though chicks produced few distress vocalizations. The pronounced and specific reaction observed indicates that adult female birds possess at least one of the essential underpinning attributes of empathy.