bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographical and host distribution patterns of Parvicapsula minibicornis (Myxozoa) small subunit ribosomal RNA genetic types
Authors: ATKINSON STEPHEN D. , JONES SIMON R. M. , ADLARD ROBERT D. , BARTHOLOMEW JERRI L. 
Published: May 2011

SUMMARYParvicapsula minibicornis is a myxozoan parasite implicated in mortalities of both juvenile and pre-spawning adult salmon in the Pacific Northwest of North America. Disease severity and presentation varies between salmon species and geographical localities. To better characterize population structure of the parasite, we sought genetic markers in the P. minibicornis ribosomal RNA gene. We compared samples from California with the type specimen from British Columbia, identified sequence variations, and then sequenced 197 samples from fish, river water and the parasite's polychaete worm host. Although DNA sequences of the parasite were >98·9% similar, there was enough variation to define 15 genotypes. All genotypes were detected in fish samples, although not in all species. A single genotype only was found in sockeye and pink salmon in the Fraser River Basin, but was not detected in sockeye from the adjacent Columbia River Basin. All coho salmon, irrespective of river basin, were infected with a unique mix of 2 genotypes. These data indicated that the P. minibicornis population exhibited strong signals of structuring by both geography and salmonid host species. Particular genotypes may correlate with disease differences seen in salmon populations in the Pacific Northwest.
Psychophysical scaling: Judgments of attributes or objects?
Authors: Lockhead Gregory R. 
Published: May 2011

AbstractPsychophysical scaling models of the form R = f(I), with R the response and I some intensity of an attribute, all assume that people judge the amounts of an attribute. With simple biases excepted, most also assume that judgments are independent of space, time, and features of the situation other than the one being judged. Many data support these ideas: Magnitude estimations of brightness (R) increase with luminance (I). Nevertheless, I argue that the general model is wrong. The stabilized retinal image literature shows that nothing is seen if light does not change over time. The classification literature shows that dimensions often combine to produce emergent properties that cannot be described by the elements in the stimulus. These and other effects cannot be adjusted for by simply adding variables to the general model because some factors do not combine linearly. The proposed alternative is that people initially judge the entire stimulus – the object in terms of its environment. This agrees with the constancy literature that shows that objects and their attributes are identified through their relations to other aspects of the scene. That the environment determines judgments is masked in scaling studies where the standard procedure is to hold context constant. In a typical brightness study (where different lights are presented on the same background on different trials) the essential stimulus might be the intensity of the light or a difference between the light and the background. The two are perfectly confounded. This issue is examined in the case of audition. Judgments of the loudness of a tone depend on how much that tone differs from the previous tone in both pitch and loudness. To judge loudness (and other attributes) people first seem to process the stimulus object in terms of differences between it and other aspects in the situation; only then do they assess the feature of interest. Psychophysical judgments will therefore be better interpreted by theories of attention that are based in biology or psychology than those (following Fechner) that are based in classical physics.
What connectionist models learn: Learning and representation in connectionist networks
Authors: Hanson Stephen José , Burr David J. 
Published: May 2011

AbstractConnectionist models provide a promising alternative to the traditional computational approach that has for several decades dominated cognitive science and artificial intelligence, although the nature of connectionist models and their relation to symbol processing remains controversial. Connectionist models can be characterized by three general computational features: distinct layers of interconnected units, recursive rules for updating the strengths of the connections during learning, and “simple” homogeneous computing elements. Using just these three features one can construct surprisingly elegant and powerful models of memory, perception, motor control, categorization, and reasoning. What makes the connectionist approach unique is not its variety of representational possibilities (including “distributed representations”) or its departure from explicit rule-based models, or even its preoccupation with the brain metaphor. Rather, it is that connectionist models can be used to explore systematically the complex interaction between learning and representation, as we try to demonstrate through the analysis of several large networks.
Functional specialization in the lower and upper visual fields in humans: Its ecological origins and neurophysiological implications
Authors: Previc Fred H. 
Published: May 2011

AbstractFunctional specialization in the lower and upper visual fields in humans is analyzed in relation to the origins of the primate visual system. Processing differences between the vertical hemifields are related to the distinction betweennear(peripersonal) andfar(extrapersonal) space, which are biased toward the lower and upper visual fields, respectively.Nonlinear/globalprocessing is required in the lower visual field in order to pergeive the optically degraded and diplopic images in near vision, whereas objects in far vision are searched for and recognized primarily usinglinear/localperceptual mechanisms. The functional differences between near and far visual space are correlated with their disproportionate representations in thedorsalandventraldivisions of visual association cortex, respectively, and in themagnocellularandparvocellularpathways that project to them. Advances in far visual capabilities and forelimb manipulatory skills may have led to a significant enhancement of these functional specializations.
Provenance changes between recent and glacial-time sediments in the Amundsen Sea embayment, West Antarctica: clay mineral assemblage evidence
Authors: Ehrmann Werner , Hillenbrand Claus-Dieter , Smith James A. , Graham Alastair G.C. , Kuhn Gerhard , Larter Robert D. 
Published: May 2011

AbstractThe Amundsen Sea embayment is a probable site for the initiation of a future collapse of the West Antarctic Ice Sheet. This paper contributes to a better understanding of the transport pathways of subglacial sediments into this embayment at present and during the last glacial period. It discusses the clay mineral composition of sediment samples taken from the seafloor surface and marine cores in order to decipher spatial and temporal changes in the sediment provenance. The most striking feature in the present-day clay mineral distribution is the high concentration of kaolinite, which is mainly supplied by the Thwaites Glacier system and indicates the presence of hitherto unknown kaolinite-bearing sedimentary strata in the hinterland, probably in the Byrd Subglacial Basin. The main illite input is via the Pine Island Glacier. Smectite originates from the erosion of volcanic rocks in Ellsworth Land and western Marie Byrd Land. The clay mineral assemblages in diamictons deposited during the last glacial period are distinctly different from those in corresponding surface sediments. This relationship indicates that glacial sediment sources were different from modern ones, which could reflect changes in the catchment areas of the glaciers and ice streams.
TRANSCRITICAL FLOW PAST AN OBSTACLE
Authors: GRIMSHAW R. 
Published: May 2011

AbstractIt is well known that transcritical flow past an obstacle may generate undular bores propagating away from the obstacle. This flow has been successfully modelled in the framework of the forced Korteweg–de Vries equation, where numerical simulations and asymptotic analyses have shown that the unsteady undular bores are connected by a locally steady solution over the obstacle. In this paper we present an overview of the underlying theory, together with some recent work on the case where the obstacle has a large width.
Pension costs and liabilities for UK-regulated utilities
Authors: HUGHES GORDON 
Published: May 2011

AbstractThis paper argues that a substantial portion of the risks associated with the defined benefit (DB) pension schemes operated by regulated utilities in the UK will, in practice, fall on customers via the tariffs that they pay for regulated goods and services. It examines the assumptions made by regulated companies in their FRS 17 valuations. These assumptions generate parameters that systematically understate both the present value of pension liabilities and current service costs. These are re-estimated using the risk-free real rate of discount and compatible assumptions. On this basis, the total pension deficit for the sample increased from £12.7 billion to £56.3 billion in 2009, equivalent to about 110% of regulated revenues. Further, the cost of current service for 2008–09 was 20% higher than total contributions in the year, despite large top-up contributions. If contributions were increased to cover current service costs and to eliminate pension deficits over a period of 10 years, the additional contributions would amount to 235% of actual contributions or 13% of regulated revenues implying a significant increase in regulated charges. Companies in the communications and transport sectors face the largest adjustments in addressing the problems of underfunded pension schemes.
Visualizing classification of natural video sequences using sparse, hierarchical models of cortex.
Authors: Brumby Steven , Ham Michael , Landecker Will , Kenyon Garrett , Bettencourt Luís 
Published: May 2011

AbstractRecent work on hierarchical models of visual cortex has reported state-of-the-art accuracy on whole-scene labeling using natural still imagery. This raises the question of whether the reported accuracy may be due to the sophisticated, non-biological back-end supervised classifiers typically used (support vector machines) and/or the limited number of images used in these experiments. In particular, is *the model classifying features from the object or the background? Previous work (Landecker, Brumby, et al., COSYNE 2010) proposed tracing the spatial support *of a classifier’s decision back through a hierarchical cortical model to determine which parts of the image contributed to the classification, compared to the positions of objects in the scene. In this way, we can go beyond standard measures of accuracy to provide tools for visualizing and analyzing high-level object classification. We now describe new work exploring the extension of these ideas to detection of objects in video sequences of natural scenes.
Estimation of oxidative status in lymphocytes of type2 diabetes mellitus patients
Authors: Arya Awadhesh K , Tripathi Kamlakar 
Published: May 2011

AbstractIntroduction: Diabetes mellitus (DM) is a group of metabolic disorders which opens the door for many diseases leading to various complications like neuropathy, nephropathy and retinopathy. Type 2 diabetes mellitus (T2DM) is associated with elevated level of oxidative stress, which is one of the most important factors responsible for the development of chronic complications of this disease. Antioxidants like reduced glutathione (GSH), superoxide dismutase (SOD) and catalase protects cells against oxidative damage.
Purpose:
Our present study suggests that hyperglycemia induced oxidative stress leads to various complications in T2DM patients. Here we investigated oxidative stress markers in lymphocytes of healthy control and diabetes mellitus patients.

Methods:
In the present study, 40 patients with T2DM (group A), aged 35-65 years and 30 healthy individuals (group B) of the same age group were included. Lymphocytes were isolated by using ficoll hypaque from heparinised blood obtained from all the participants in this study. Lymphocyte SOD, Catalase, Glutathione and MDA were estimated by using an ELISA reader.

Results:
SOD activity was higher in group B (98.97 ± 8.01) as compared with group A (49.71 ± 5.85);whereas catalase (61.50 ± 8.79 vs 76.33 ± 6.80) and glutathione (44.22 ± 6.85 vs 63.61 ± 8.89) amount was reduced in the same group as compared with healthy control. Lipid peroxidation was higher in group B (13.43 ± 3.99) as compared with healthy control (9.89 ± 2.59).

Conclusions:
Hyperglycemia induces the oxidative stress condition inside the lymphocytes which stimulates cell death for various cells including lymphocytes. Our data collectively confirm a significant decrease in lymphocyte GSH and catalase activity as well as an increase in activity of SOD and MDA reflecting elevated oxidative stress in the diabetic state.
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
Authors: Hou Tingjun , Li Youyong , Wang Wei 
Published: May 2011

Abstract
Motivation: Favorable interaction between the regulatory subunit of the cAMP-dependent protein kinase (PKA) and a peptide in A-kinase anchoring proteins (AKAPs) is critical for translocating PKA to the subcellular sites where the enzyme phosphorylates its substrates. It is very hard to identify AKAPs peptides binding to PKA due to the high sequence diversity of AKAPs.
Results: We propose a hierarchical and efficient approach, which combines molecular dynamics (MD) simulations, free energy calculations, virtual mutagenesis (VM) and bioinformatics analyses, to predict peptides binding to the PKA RIIα regulatory subunit in the human proteome systematically. Our approach successfully retrieved 15 out of 18 documented RIIα-binding peptides. Literature curation supported that many newly predicted peptides might be true AKAPs. Here, we present the first systematic search for AKAP peptides in the human proteome, which is useful to further experimental identification of AKAPs and functional analysis of their biological roles.
Contact: tingjunhou@hotmail.com; tjhou@suda.edu.cn; wei-wang@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sensitive and fast mapping of di-base encoded reads
Authors: Hormozdiari Farhad , Hach Faraz , Sahinalp S. Cenk , Eichler Evan E. , Alkan Can 
Published: May 2011

Abstract
Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of read mapping are crucial to determining the full spectrum of single nucleotide variants (SNVs) as well as structural variants (SVs) in the donor genomes analyzed.
Results: We present drFAST, a read mapper designed for di-base encoded ‘color-space’ sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. We show that drFAST is more sensitive in comparison to all commonly used aligners such as Bowtie, BFAST and SHRiMP. drFAST is also faster than both BFAST and SHRiMP and achieves a mapping speed comparable to Bowtie.
Availability: The source code for drFAST is available at http://drfast.sourceforge.net
Contact: calkan@u.washington.edu
Methaemalbumin formation in sickle cell disease: effect on oxidative protein modification and HO‐1 induction
Authors: Hanson Madelyn S. , Piknova Barbora , Keszler Agnes , Diers Anne R. , Wang Xunde , Gladwin Mark T. , Hillery Cheryl A. , Hogg Neil 
Published: May 2011

SummaryNormally, cell free haemoglobin is bound by haptoglobin and efficiently cleared. However, the chronic haemolysis in sickle cell disease (SCD) overwhelms haptoglobin binding capacity and protein turnover, resulting in elevated cell free haemoglobin. Cell free haemoglobin acts as both a scavenger of vasoactive nitric oxide and a pro‐oxidant. In addition, methaemoglobin (metHb) releases the haem moiety, which can bind to albumin to form methaemalbumin (metHSA). This study used electron paramagnetic resonance to detect metHSA in SCD plasma and demonstrated that haptoglobin prevents haem transfer from metHb to HSA. MetHSA may either provide a second line of defence against haemoglobin/haem‐mediated oxidation or contribute to the pro‐oxidant environment of SCD plasma. We demonstrated that HSA inhibited oxidative protein modification induced by metHb. Additionally, we showed that while metHb induced haem oxygenase 1 (HO‐1), an indicator of oxidative stress, HSA attenuated metHb induction of this enzyme, thereby limiting the potential benefits of HO‐1. Furthermore, HO‐1 induction by metHSA was less than HO‐1 induction by equimolar metHb not bound to albumin. Our findings confirm the presence of metHSA in SCD and suggest that haem transfer from metHb to HSA reduces the oxidative effects of free haemoglobin/haem on endothelium with both beneficial (reduced protein oxidation) and potentially harmful (reduced HO‐1 induction) outcomes.
C‐type lectins on macrophages participate in the immunomodulatory response to Fasciola hepatica products
Authors: Guasconi Lorena , Serradell Marianela C. , Garro Ana P. , Iacobelli Luciana , Masih Diana T. 
Published: May 2011

SummaryFasciola hepatica releases excretory–secretory products (FhESP), and immunomodulatory properties have been described for the carbohydrates present in these parasite products. The interaction of FhESP with the innate immune cells, such as macrophages, is crucial in the early stage of infection. In this work we observed that peritoneal macrophages from naive BALB/c mice stimulated in vitro with FhESP presented: an increased arginase activity as well as Arginase I expression, and high levels of transforming growth factor‐β and interleukin‐10. A similar macrophage population was also observed in the peritoneum of infected mice. A partial inhibition of the immunomodulatory effects described above was observed when macrophages were pre‐incubated with Mannan, anti‐mannose receptor, Laminarin or anti‐Dectin‐1, and then stimulated with FhESP. In addition, we observed a partial inhibition of these effects in macrophages obtained from mice that were intraperitoneally injected with Mannan or Laminarin before being infected. Taken together, these results suggest the participation of at least two C‐type lectin receptors, mannose receptor and Dectin‐1, in the interaction of FhESP with macrophages, which allows this parasite to induce immunoregulatory effects on these important innate immune cells and may constitute a crucial event for extending its survival in the host.
Production of pure protein and antibodies and development of immunoassays to detect Ara h 3 levels in peanut varieties
Authors: Hurlburt Barry K. , Schmitt David , Isleib Thomas G. , Cheng Hsiaopo , Garvey Cathryn , Koenig Robbin L. , Maleki Soheila J. 
Published: May 2011

SummaryPeanuts are one of the most allergenic foods and are widespread in western food products. Therefore, there has been intense research into the allergic nature of the proteins involved. Ara h 3 is one of three immunodominant allergenic proteins. It is a 60‐kDa protein, which forms following cleavage of the preprotein and association of the resultant 40‐ and 20‐kDa subunits. The large subunit has been shown to harbour most of the reactive epitopes and has the protein fold likely responsible for its trypsin inhibitor activity. In this work, we have developed a method for the high‐level expression and purification of recombinant Ara h 3 40‐kDa subunit. Specific antibodies have been produced and applied to the secondary and tertiary screens of hundreds of peanut cultivars. Several of these cultivars were identified that have significantly reduced accumulation of Ara h 3.
Evaluation of the fouling phenomenon in the membrane clarification of black mulberry juice
Authors: Hojjatpanah Ghazaleh , Emam‐Djomeh Zahra , Ashtari Ahmad Kalbasi , Mirsaeedghazi Hossein , Omid Mahmoud 
Published: May 2011

SummaryMixed cellulose ester (MCE) flat membranes were used to clarify black mulberry juice, the yield of which was limited by fouling. The effects of membrane pore size (0.025, 0.1 and 0.22 μm), transmembrane pressure (0.5, 1, 1.5 and 200 kPa), and cross‐flow velocity (0.1, 0.2, 0.3 and 0.4 m s−1) on membrane fouling were evaluated; the results showed that fouling increased with increased pore size and pressure, and decreased with increased velocity. Analysis of different resistances showed that both reversible and irreversible fouling resistances have an important role in fouling‐resistance changes. There is no cake resistance in all processes. Microstructure analysis of membrane using scanning electron microscopy confirmed the theory that intermediate blocking was the dominant fouling mechanism in MCE 0.025 μm, and standard blocking was the dominant mechanism in MCE 0.1 and 0.22 μm.
Preparation and characteristics of yak casein hydrolysate–iron complex
Authors: Wang Xu , Li Ming , Li Min , Mao Xueying , Zhou Jie , Ren Fazheng 
Published: May 2011

SummaryThe effect of mass ratio between yak casein hydrolysate and FeSO4, reaction temperature, pH and holding time on ferrous‐binding capacity of yak casein hydrolysate was investigated. Iron‐releasing percentage and structural characteristics of the formed yak casein hydrolysate–iron complex were also examined. Results showed that casein hydrolysates with different hydrolysis degrees (DH) possessed different ferrous‐binding capacities with the highest of 7‐h hydrolysate. The optimal binding conditions between yak casein hydrolysate and iron are mass ratio of casein hydrolysate to FeSO4 of 15:1 for 20 min at 40 °C and pH 6.0. The principal binding site for Fe2+ in yak casein hydrolysate consists of the carboxylate groups and amide groups. Compared with ferrous sulphate, yak casein hydrolysate–iron complex has higher iron‐releasing percentage at basic conditions, such as pH 7.0, 7.5 and 8.0. Ferrous‐iron enriched casein hydrolysate, i.e. yak casein hydrolysate–iron complex, may have great potential as an effective delivery vehicle of bioavailable iron.