bluuebunny/crossref_metadata_2025 huggingface dataset:
Seasonal variations in plant mineral content and free-choice minerals consumed by deer
Authors: Estevez J. A. , Landete-Castillejos T. , García A. J. , Ceacero F. , Martínez A. , Gaspar-López E. , Calatayud A. , Gallego L.
Published: April 2010

The aim of this study was to assess the seasonal differences in mineral contents of plants often consumed by wild red deer located in a fenced game estate, south-eastern Spain. Forage plants were sampled throughout 1 year and analysed for macro and trace mineral concentrations. We also offered a cafeteria set of supplemented minerals to assess whether: (i) intake reflected seasonal reductions in plant content of specific minerals; or (ii) intake of mineral supplements responded to increased deer demand of minerals as a result of greater seasonal needs likely arising from lactation, antler growth or skeletal growth.
Although no significant seasonal trend was found in mineral distributions of plants, our study suggested that concentrations of K, Mg, Mn, Na, P, Cu and Zn were usually low in plants available to, and consumed by, deer in the study area. In addition, Cu concentration was marginally deficient when compared with the published requirements for other subspecies of red deer. The cafeteria study showed that free-ranging deer had a strong preference for sodium compounds and zinc sulfate, a much weaker attraction to calcium iodate, and no intake in calcium phosphates, Mg and Fe. Consumption of supplemented minerals by deer was maximum in spring and summer and moderate during autumn and winter.
Rather than increasing intake of minerals in response to their content in plants, deer may be responding to increased metabolic requirements during antler growth, late gestation and early lactation. Supplementation of mineral compounds is recommended, particularly in the spring–summer period, when the physiological activity is high.
Experimental validation of the Intergovernmental Panel on Climate Change default values for ruminant-derived methane and its carbon-isotope signature
Authors: Klevenhusen F. , Bernasconi S. M. , Kreuzer M. , Soliva C. R.
Published: April 2010

Two aspects regarding the ruminant’s contribution to global methane (CH4) emissions were investigated: (i) testing the accuracy of the Intergovernmental Panel on Climate Change default values for dairy cows fed different diet types and differing slurry storage temperatures; and (ii) providing carbon-isotope (C-isotope) signature data to contribute information on the characteristics of ruminant-derived CH4 as global source. The experimental diets, fed to 18 dairy cows, were separated into forage-only (hay, C3 plant) and forage-concentrate diets (barley, C3 plant; maize, C4 plant). Accumulated slurry was stored at either 14 or 27°C. The hay diet had the highest CH4 conversion rate (Ym 7.9%). Negligible amounts of CH4 were emitted from slurries stored at low temperature. No diet effect was found at 27°C (~33 L/kg volatile solids). The isotope ratios of enteric CH4 averaged −67.7‰ (C3 plants) and −57.4‰ (C4; maize). High temperature slurry storage resulted in different enrichment factors ϵCO2-CH4 for maize (33.2‰) and hay (35.9‰). Compared with the Intergovernmental Panel on Climate Change default values for Ym and slurry CH4 emission the results gained in the present experiment were higher and lower, respectively. Slurry-derived CH4 was less depleted in 13C than enteric CH4, which decreases the usefulness of this signature for global ruminant-derived CH4.
Preliminary genetic analyses of voluntarily supplied disease data in Australian dairy herds
Authors: Haile-Mariam M. , Goddard M. E.
Published: April 2010

Health disorders data collected from Australian dairy herds were analysed to estimate incidence levels and genetic parameters for some diseases traits and to examine the consequence of selection for Australian profit ranking (the economic index in Australia) and other economic traits on incidence of some diseases. Data on disease problems including udder, leg, reproductive and ‘all disorders’ were extracted from the Australian Dairy Herd Improvement Scheme database for cows that calved in 2007 and 2008 and were analysed fitting a linear sire model.
The occurrence of disease problems was as high as 0.3 if ‘all disorders’ were put into one group. Five percent of the cows that calved showed leg problems and the incidence of udder problems was ~0.13. The heritability of all disease problems ranged from 0.01 for reproductive problems to 0.03 for udder problems. The results showed that selection on milk yield traits will likely increase the frequency of all health disorders. Although selection on udder depth and somatic cell count helps to mitigate the possible genetic deterioration in udder problems, it is unlikely to avoid it totally. Therefore, more effort to collect and analyse health event data from Australia dairy herds could help to better design genetic and environmental measures to reduce the consequence of health problems.
Evaluation of lablab and velvet bean fallows in a maize production system for improved livestock feed supply in semiarid tropical Kenya
Authors: Njarui D. M. G. , Mureithi J. G.
Published: April 2010

The mixed crop–livestock farming systems of semiarid tropical Kenya are characterised by low livestock feed supply. The contribution of lablab and velvet bean to fodder production in a maize production system was investigated in the eastern region of Kenya. The experiment was run in three cycles, where each cycle consisted of a short legume fallow phase of ~6 months, followed by a maize-cropping phase. At the end of the fallow phase, the legume herbage was incorporated in soil at three levels; 0, 50 and 100% of total DM yield and maize planted. Maize yield from the legume fallow plots was compared with maize grown after natural fallow and maize top-dressed with 40 kg nitrogen/ha and nil nitrogen fertiliser. Overall, herbage DM yield was highest in velvet bean (3.9 t/ha) followed by lablab (3.4 t/ha) and lowest in natural fallow (2.2 t/ha). Mean crude protein from velvet bean was 13.5% of DM, which was significantly (P < 0.05) higher than that of lablab (8.4% of DM) and natural weedy fallow (3.5% of DM). Maize grain yield following lablab fallow was 38% (3569 kg/ha) and 27% (1810 kg/ha) in short rains (SR) 2002 and SR 2004, respectively, higher than maize succeeding natural fallow. However, maize planted after velvet bean fallow was 43% (3728 kg/ha) and 29.4% (1828 kg/ha) in SR 2002 and SR 2004, respectively, higher than in maize grown after natural fallow. Generally, the highest maize yield among the fallows was recorded in plots where legumes were incorporated in soil at 50% of total DM implying that the other 50% was available for livestock feed. Maize stovers DM yields were highest at the higher (100%) and middle (50%) level of legume incorporation, and yields were more than those from natural weedy fallow. Maize production under the legume fallow system was more profitable than from natural weedy fallows. It was concluded that if lablab and velvet bean are integrated in cropping systems as fallows, they can provide highly nutritious livestock feeds and improve maize yield and are recommended in the maize production systems within semiarid tropical Kenya.
Relationships between immune indicators of parasitic gastroenteritis, nematode burdens and faecal dry matter in sheep
Authors: Williams A. R. , Palmer D. G. , Williams I. H. , Vercoe P. E. , Emery D. L. , Karlsson L. J. E.
Published: April 2010

Immune-mediated scouring in sheep is a mucosal hypersensitivity response caused by ingesting infective parasite larvae. In this experiment we tested the hypothesis that levels of parasite-specific antibodies and also interleukin-5 (IL-5) would be negatively correlated with worm numbers, but also faecal dry matter (FDM), in parasite-resistant Merino sheep. Forty Merino rams were challenged with Trichostrongylus colubriformis and Teladorsagia circumcincta larvae every day for 6 weeks, after which they were euthanised and total worm burdens determined. Faecal samples were taken for measurement of worm egg counts and FDM. Serum was collected from the rams before and after the larval challenge commenced, and levels of ovine immunoglobulin light chain, IgG, IgM, IgA and IgE specific for T. colubriformis and T. circumcincta as well as IL-5 were determined by sandwich enzyme-linked immunosorbent assay. IL-5 and all serum antibodies apart from T. colubriformis-specific light chain were significantly increased by the larval challenge. However, none of the antibodies, or IL-5, was correlated with FDM. Negative correlations were observed between the number of adult T. circumcincta and antibody levels; however, there was little relationship between antibodies and numbers of T. colubriformis. It was concluded that serum antibody levels are a poor indicator of the susceptibility of sheep to immune-mediated scouring. Because of these results, sheep breeders should continue to select for low worm egg count and focus on phenotypic indicators of scouring, such as dags, as a means to reduce diarrhoea.
Preliminary study of the changes in rumen bacterial populations from cattle intoxicated with young oak (Quercus pyrenaica) leaves
Authors: Belenguer A. , Hervás G. , Yáñez-Ruiz D. R. , Toral P. G. , Ezquerro C. , Frutos P.
Published: April 2010

Intoxication of grazing cattle occurs repeatedly when they consume large amounts of young oak leaves (OL), which are rich in hydrolysable tannins (HT), due to a shortage of other feed resources. The HT are antimicrobial, although some rumen bacteria can resist or degrade them into potentially toxic or harmless metabolites. To study the effect of the administration of HT-rich OL (Quercus pyrenaica) after a severe feed restriction on the rumen bacterial community and monitor the variations in some bacterial groups that are potentially able to resist or metabolise tannins, three ruminally cannulated bulls were initially fed grass hay and then subjected to a severe 8-day feed restriction period, before receiving OL for 6 days. Then, the animals were again offered grass hay for 12 more days. Rumen contents were sampled throughout the experiment. Quantitative real-time polymerase chain reaction and terminal restriction fragment length polymorphism were used to monitor the bacterial dynamics. Animal 1 was not intoxicated and showed lower relative abundances of Streptococcus bovis initially and after the OL administration than Animals 2 and 3, which showed acute signs of intoxication. The genus Prevotella increased its abundance with the OL administration, whereas Selenomonas ruminantium was reduced. The bacterial terminal restriction fragment length polymorphism profile of Animal 1 clustered initially separately from Animals 2 and 3 and was less affected by the feed restriction period. These results showed that the effect of the consumption of HT-rich OL after a severe feed restriction is highly variable in cattle and might rely on the individual composition of the microbiota colonising the rumen.
Supramolecular Chemistry of Pyronines B and Y, β-Cyclodextrin and Linked β-Cyclodextrin Dimers
Authors: Ngo Huy T. , Clements Philip , Easton Christopher J. , Pham Duc-Truc , Lincoln Stephen F.
Published: April 2010

The complexation of cationic pyronine B (PB+) and pyronine Y (PY+) by β-cyclodextrin (βCD) and two linked βCD dimers, N,N′-bis((2AS,3AS)-3A-deoxy-β-cyclodextrin-3A-yl)succinamide, 33βCD2suc, and N,N′-bis(6A-deoxy-β-cyclodextrin-6A-yl)succinamide, 66βCD2suc, in aqueous solution has been studied by UV-vis, fluorescence, and 1H NMR spectroscopy. The complexation constants for the 1:1 complexes: βCD.PB+, 33βCD2suc.PB+, 66βCD2suc.PB+, and the analogous PY+ complexes are reported as are the dimerization constants for PB+ and PY+. The modes of complexation, dimerization, and fluorescence quenching are discussed.
Orthogonally Protected Monosaccharide Building Blocks for Solid Phase Production of Diversity Oriented Libraries
Authors: Rajaratnam Premraj , Gupta Praveer , Katavic Peter , Kuipers Krystle , Huyh Ngoc , Ryan Sarah , Falzun Tania , Tometzki Gerrald B. , Bornaghi Laurent , Le Thanh Giang , Abbenante Giovanni , Liu Ligong , Meutermans Wim , Wimmer Norbert , West Michael L.
Published: April 2010

The large scale synthesis of three orthogonally protected monosaccharide scaffolds suitable for use in the solid phase preparation of large diversity libraries is presented. Scaffolds based on 2-amino-2-deoxy-d-glucopyranose, 2-amino-2-deoxy-d-allopyranose, and 2,4-diamino-2,4-dideoxy-d-galactopyranose were prepared in good yield and with minimal chromatographic purification from commercially available methyl 2-azido-2-deoxy-1-thio-β-d-glucopyranose and methyl 2-amino-2-deoxy-1-thio-β-d-glucopyranose.
Supramolecular Polymers
Authors: de Greef Tom F.A. , Meijer E. W.
Published: April 2010

In the past few decades, supramolecular polymers have emerged as novel materials with a wide variety of different functions. In this essay we reflect on the history of supramolecular polymers, their function in various applications and the challenges to be met in the near future.
An Aqueous Supramolecular Side-Chain Polymer Designed for Molecular Loading
Authors: Geng Jin , Jiao Dezhi , Rauwald Urs , Scherman Oren A.
Published: April 2010

Hydrophilic copolymers containing recognition motifs based on 2-naphthol moieties in their side chains for the self-assembly with cucurbit[8]uril (CB[8]), have been prepared by reversible addition–fragmentation chain transfer polymerization. Self-assembly of the copolymer with both redox sensitive hydrophilic and hydrophobic viologen derivatives in the presence of CB[8] has been investigated.
Idiosyncratic and systematic aspects of spatial representations in the macaque parietal cortex
Authors: Chang Steve W. C. , Snyder Lawrence H.
Published: April 2010

The sensorimotor transformations for visually guided reaching were originally thought to take place in a series of discrete transitions from one systematic frame of reference to the next with neurons coding location relative to the fixation position (gaze-centered) in occipital and posterior parietal areas, relative to the shoulder in dorsal premotor cortex, and in muscle- or joint-based coordinates in motor output neurons. Recent empirical and theoretical work has suggested that spatial encodings that use a range of idiosyncratic representations may increase computational power and flexibility. We now show that neurons in the parietal reach region use nonuniform and idiosyncratic frames of reference. We also show that these nonsystematic reference frames coexist with a systematic compound gain field that modulates activity proportional to the distance between the eyes and the hand. Thus, systematic and idiosyncratic signals may coexist within individual neurons.
Self-similarity and scaling in forest communities
Authors: Simini Filippo , Anfodillo Tommaso , Carrer Marco , Banavar Jayanth R. , Maritan Amos
Published: April 2010

Ecological communities exhibit pervasive patterns and interrelationships between size, abundance, and the availability of resources. We use scaling ideas to develop a unified, model-independent framework for understanding the distribution of tree sizes, their energy use, and spatial distribution in tropical forests. We demonstrate that the scaling of the tree crown at the individual level drives the forest structure when resources are fully used. Our predictions match perfectly with the scaling behavior of an exactly solvable self-similar model of a forest and are in good accord with empirical data. The range, over which pure power law behavior is observed, depends on the available amount of resources. The scaling framework can be used for assessing the effects of natural and anthropogenic disturbances on ecosystem structure and functionality.
More than one kind of inference: Re-examining what's learned in feature inference and classification
Authors: Sweller Naomi , Hayes Brett K.
Published: April 2010

Three studies examined how task demands that impact on attention to typical or atypical category features shape the category representations formed through classification learning and inference learning. During training categories were learned via exemplar classification or by inferring missing exemplar features. In the latter condition inferences were made about missing typical features alone (typical feature inference) or about both missing typical and atypical features (mixed feature inference). Classification and mixed feature inference led to the incorporation of typical and atypical features into category representations, with both kinds of features influencing inferences about familiar (Experiments 1 and 2) and novel (Experiment 3) test items. Those in the typical inference condition focused primarily on typical features. Together with formal modelling, these results challenge previous accounts that have characterized inference learning as producing a focus on typical category features. The results show that two different kinds of inference learning are possible and that these are subserved by different kinds of category representations.
The effect of word position on eye-movements in sentence and paragraph reading
Authors: Kuperman Victor , Dambacher Michael , Nuthmann Antje , Kliegl Reinhold
Published: April 2010

The present study explores the role of the word position-in-text in sentence and paragraph reading. Three eye-movement data sets based on the reading of Dutch and German unrelated sentences reveal a sizeable, replicable increase in reading times over several words at the beginning and the end of sentences. The data from the paragraph-based English-language Dundee corpus replicate the pattern and also indicate that the increase in inspection times is driven by the visual boundaries of the text organized in lines, rather than by syntactic sentence boundaries. We argue that this effect is independent of several established lexical, contextual, and oculomotor predictors of eye-movement behaviour. We also provide evidence that the effect of word position-in-text has two independent components: a start-up effect, arguably caused by a strategic oculomotor programme of saccade planning over the line of text, and a wrap-up effect, originating in cognitive processes of comprehension and semantic integration.
When attractiveness demands longer looks: The effects of situation and gender
Authors: Leder Helmut , Tinio Pablo P. L. , Fuchs Isabella M. , Bohrn Isabel
Published: April 2010

We investigated how aesthetics guides our exploration of the environment. We embedded attractive and nonattractive faces into complex, real-world scenes and measured eye movements during scene viewing. We examined whether attractive faces would elicit longer looks, which would suggest that the aesthetic response orients people toward the rewarding and pleasing aspects of the environment. Experiment 1 showed that mean fixation, mean first fixation, and total fixation durations were longer to attractive faces, and fixations were longest to female faces and by female perceivers. In Experiment 2, we examined whether these effects of attractiveness are sensitive to situational factors. When perceivers were subjected to a threat or social approach manipulation prior to viewing the scenes, we confirmed specific hypotheses concerning the two manipulations. In accordance with the hypothesis that males have higher aggression potential than females, there were no differences in fixation durations between attractive and nonattractive male faces in the threat condition. On the other hand, in the social approach condition, both female and male attractive faces received longer looks. These results suggest that the aesthetic response orients people not only to the pleasing aspects of their environment, but also to those features that are adaptively relevant.
Judgements of time to contact are affected by rate of appearance of visible texture
Authors: Jacobs David M. , Díaz Alex
Published: April 2010

More fine-grained texture becomes visible if the distance between an observer and an object or surface is reduced. This article illustrates with a schematic example that the inverse rate of the relative appearance of visible texture provides information about time to contact if the observer has a constant visual acuity and the texture has a certain scale-independent structure. An experiment is reported in which texture appearance was manipulated. Participants were asked to make forced-choice time-to-contact judgements. A small but significant effect indicates that the judgements were affected by the rate of appearance of the texture. It is concluded that observers use this type of information.
Meiotic Cohesin Promotes Pairing of Nonhomologous Centromeres in Early Meiotic Prophase
Authors: Chuong Hoa , Dawson Dean S.
Published: April 2010

A period of pairing between nonhomologous centromeres occurs early in meiosis in a diverse collection of organisms. This early, homology-independent, centromere pairing, referred to as centromere coupling in budding yeast, gives way to an alignment of homologous centromeres as homologues synapse later in meiotic prophase. The regulation of centromere coupling and its underlying mechanism have not been elucidated. In budding yeast, the protein Zip1p is a major component of the central element of the synaptonemal complex in pachytene of meiosis, and earlier, is essential for centromere coupling. The experiments reported here demonstrate that centromere coupling is mechanistically distinct from synaptonemal complex assembly. Zip2p, Zip3p, and Red1p are all required for the assembly of Zip1 into the synaptonemal complex but are dispensable for centromere coupling. However, the meiotic cohesin Rec8p is required for centromere coupling. Loading of meiotic cohesins to centromeres and cohesin-associated regions is required for the association of Zip1 with these sites, and the association of Zip1 with the centromeres then promotes coupling. These findings reveal a mechanism that promotes associations between centromeres before the assembly of the synaptonemal complex, and they demonstrate that chromosomes are preloaded with Zip1p in a manner that may promote synapsis.
The Adipose-derived Stem Cell: Looking Back and Looking Ahead
Authors: Zuk Patricia A.
Published: April 2010

In 2002, researchers at UCLA published a manuscript in Molecular Biology of the Cell describing a novel adult stem cell population isolated from adipose tissue—the adipose-derived stem cell (ASC). Since that time, the ASC has gone on to be one of the most popular adult stem cell populations currently being used in the stem cell field. With multilineage mesodermal potential and possible ectodermal and endodermal potentials also, the ASC could conceivably be an alternate to pluripotent ES cells in both the lab and in the clinic. In this retrospective article, a historical perspective on the ASC is given together with exciting new applications for the stem cell being considered today.
Mad3 Negatively Regulates B Cell Differentiation in the Spleen by Inducing Id2 Expression
Authors: Gore Yael , Lantner Frida , Hart Gili , Shachar Idit
Published: April 2010

Immature B cells migrate to the spleen where they differentiate into mature cells. This final maturation step is crucial to enable B cells to become responsive to antigens and to participate in the immune response. Previously, we showed that Id2 acts as a negative regulator of the differentiation of immature B cells occurring in the spleen. Id2 expression has been found to depend on Myc–Max–Mad transcriptional complexes in mammary epithelial cells. Nearly all studies to date have shown that Mad proteins inhibit proliferation, presumably by antagonizing the function of Myc proteins. In the current study, we followed the Mad family members during peripheral B cell differentiation. We show that Mad3 actively regulates B cell differentiation. Our results demonstrate that high expression levels of Mad3 in immature B cells induce Id2 expression, which inhibits transcription of genes essential for B cell differentiation. During their differentiation to mature cells, B cells reduce their Mad3 expression, enabling the maturation process to occur.
The Mobile FG Nucleoporin Nup98 Is a Cofactor for Crm1-dependent Protein Export
Authors: Oka Masahiro , Asally Munehiro , Yasuda Yoshinari , Ogawa Yutaka , Tachibana Taro , Yoneda Yoshihiro
Published: April 2010

Nup98 is a mobile nucleoporin that forms distinct dots in the nucleus, and, although a role for Nup98 in nuclear transport has been suggested, its precise function remains unclear. Here, we show that Nup98 plays an important role in Crm1-mediated nuclear protein export. Nuclear, but not cytoplasmic, dots of EGFP-tagged Nup98 disappeared rapidly after cell treatment with leptomycin B, a specific inhibitor of the nuclear export receptor, Crm1. Mutational analysis demonstrated that Nup98 physically and functionally interacts with Crm1 in a RanGTP-dependent manner through its N-terminal phenylalanine-glycine (FG) repeat region. Moreover, the activity of the Nup98-Crm1 complex was modulated by RanBP3, a known cofactor for Crm1-mediated nuclear export. Finally, cytoplasmic microinjection of anti-Nup98 inhibited the Crm1-dependent nuclear export of proteins, concomitant with the accumulation of anti-Nup98 in the nucleus. These results clearly demonstrate that Nup98 functions as a novel shuttling cofactor for Crm1-mediated nuclear export in conjunction with RanBP3.
partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction
Authors: Molinaro Annette M. , Lostritto Karen , van der Laan Mark
Published: April 2010

Motivation: Until now, much of the focus in cancer has been on biomarker discovery and generating lists of univariately significant genes, as well as epidemiological and clinical measures. These approaches, although significant on their own, are not effective for elucidating the synergistic qualities of the numerous components in complex diseases. These components do not act one at a time, but rather in concert with numerous others. A compelling need exists to develop analytically sound and computationally advanced methods that elucidate a more biologically meaningful understanding of the mechanisms of cancer initiation and progression by taking these interactions into account.

Results: We propose a novel algorithm, partDSA, for prediction when several variables jointly affect the outcome. In such settings, piecewise constant estimation provides an intuitive approach by elucidating interactions and correlation patterns in addition to main effects. As well as generating ‘and’ statements similar to previously described methods, partDSA explores and chooses the best among all possible ‘or’ statements. The immediate benefit of partDSA is the ability to build a parsimonious model with ‘and’ and ‘or’ conjunctions that account for the observed biological phenomena. Importantly, partDSA is capable of handling categorical and continuous explanatory variables and outcomes. We evaluate the effectiveness of partDSA in comparison to several adaptive algorithms in simulations; additionally, we perform several data analyses with publicly available data and introduce the implementation of partDSA as an R package.

Availability:  http://cran.r-project.org/web/packages/partDSA/index.html

Contact:  annette.molinaro@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Multilevel support vector regression analysis to identify condition-specific regulatory networks
Authors: Chen Li , Xuan Jianhua , Riggins Rebecca B. , Wang Yue , Hoffman Eric P. , Clarke Robert
Published: April 2010

Motivation: The identification of gene regulatory modules is an important yet challenging problem in computational biology. While many computational methods have been proposed to identify regulatory modules, their initial success is largely compromised by a high rate of false positives, especially when applied to human cancer studies. New strategies are needed for reliable regulatory module identification.

Results: We present a new approach, namely multilevel support vector regression (ml-SVR), to systematically identify condition-specific regulatory modules. The approach is built upon a multilevel analysis strategy designed for suppressing false positive predictions. With this strategy, a regulatory module becomes ever more significant as more relevant gene sets are formed at finer levels. At each level, a two-stage support vector regression (SVR) method is utilized to help reduce false positive predictions by integrating binding motif information and gene expression data; a significant analysis procedure is followed to assess the significance of each regulatory module. To evaluate the effectiveness of the proposed strategy, we first compared the ml-SVR approach with other existing methods on simulation data and yeast cell cycle data. The resulting performance shows that the ml-SVR approach outperforms other methods in the identification of both regulators and their target genes. We then applied our method to breast cancer cell line data to identify condition-specific regulatory modules associated with estrogen treatment. Experimental results show that our method can identify biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer.

Availability and implementation: The ml-SVR MATLAB package can be downloaded at http://www.cbil.ece.vt.edu/software.htm

Contact:  xuan@vt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
FastEpistasis: a high performance computing solution for quantitative trait epistasis
Authors: Schüpbach Thierry , Xenarios Ioannis , Bergmann Sven , Kapur Karen
Published: April 2010

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously.

Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism (SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

Availability: FastEpistasis is open source and available free of charge only for non-commercial users from http://www.vital-it.ch/software/FastEpistasis

Contact:  karen.kapur@unil.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of Feeding a Formula Supplemented With Long‐chain Polyunsaturated Fatty Acids for 14 Weeks Improves the Ex Vivo Response to a Mitogen and Reduces the Response to a Soy Protein in Infants at Low Risk for Allergy
Authors: Field Catherine J , Van Aerde John E , Goruk Susan , Clandinin M Thomas
Published: April 2010

Background and Objective:

Feeding long‐chain polyunsaturated fatty acids (LCP) influences immunity in adults; however, less is known about their effect during development. The aim of the study was to determine the effect of feeding LCP on immunity in healthy infants during the first 4 months of life.

Patients and Methods:

Formula‐fed infants were randomized at ≤14 days of age to standard term formula (Formula) or formula containing LCP (Formula+LCP). Infants exclusively fed human milk (HM) were included for comparison. At 16 weeks of age, blood was collected and phenotypes, the ability to proliferate and produce cytokines (interleukin [IL]‐2, IL‐4, IL‐6, IL‐10, IL‐12, interferon [IFN]‐γ, tumor necrosis factor [TNF]‐α, TGF‐β) after incubation with phytohemaglutinin (PHA), β‐lactoglobulin, or soy protein were measured.

Results:

Feeding LCP resulted in a higher than and more similar proliferation rate to PHA in HM‐fed infants, possibly because of a greater TH1 type cytokine response and a higher percentage of antigen mature (CD45RO+) cells (P < 0.05). The response to β‐lactoglobulin did not differ among groups. After incubation with soy protein Formula+LCP, compared with Formula produced less IL‐2 and more TNF‐α and had a higher percentage of CD8+ and a lower percentage of CD20+ (CD20+CD54+) cells poststimulation (P < 0.05). Both formula groups produced less IL‐2 after PHA, had a lower percentage of CD80+ cells, and a higher percentage of CD54+ cells after incubation with food proteins (P < 0.05).

Conclusions:

Formula‐fed infants, at low risk for allergy, respond differently to mitogen and food proteins ex vivo than those fed HM. Feeding LCP altered some of these differences in the direction that is hypothesized to confer immune benefits.
Clinical and Genetic Characteristics of Meconium Ileus in Newborns With and Without Cystic Fibrosis
Authors: Gorter RR , Karimi A , Sleeboom C , Kneepkens CMF , Heij HA
Published: April 2010

The present study compares the clinical presentation and diagnostic features of meconium ileus (MI) in newborns with and without cystic fibrosis (CF). A retrospective study of 43 patients treated in the Pediatric Surgical Center of Amsterdam was performed. Twenty‐three of the patients (53.5%) were diagnosed as having CF. Complex MI was significantly more frequent in patients without CF, and these patients had lower gestational ages and birth weights than patients with CF. All of the patients with complex MI had homozygous DF508 mutations, whereas the patients with simple MI also had other mutations. None of the patients with other mutations had complex MI. Therefore, we conclude that the clinical entity of MI represents a spectrum of underlying pathologies.
Effectiveness of Infliximab in Brazilian Children and Adolescents With Crohn Disease and Ulcerative Colitis According to Clinical Manifestations, Activity Indices of Inflammatory Bowel Disease, and Corticosteroid Use
Authors: Tiemi Juliana , Komati Saito , Sdepanian Vera Lucia
Published: April 2010

Objective:

The objective of the study was to evaluate the response to infliximab in children and adolescents with Crohn disease and ulcerative colitis up to week 22.

Patients and Methods:

A total of 21 patients with inflammatory bowel disease (IBD) received 5 mg/kg of infliximab at weeks 0, 2, 6, and 14. The following parameters were evaluated: clinical manifestations; activity indices of IBD, including the Pediatric Crohn Disease Activity Index for Crohn disease, the Lightiger Colitis Activity Index and the Pediatric Ulcerative Colitis Activity Index for ulcerative colitis, and the modified Harvey‐Bradshaw Index for Crohn disease and ulcerative colitis; and the reduction or suspension of corticosteroid use.

Results:

All of the patients had improvements in clinical manifestations after the first infusion of infliximab. At week 22, 18 of 21 (85.7%) patients were categorized as being in remission, 3 of 21 (14.3%) patients were categorized as having clinical improvement, and none of the patients were categorized as having no response. There was a statistically significant difference in all of the IBD activity indices at weeks 2, 6, 14, and 22 compared with time 0. The corticosteroid use was completely discontinued in 6 of 15 patients by week 22.

Conclusions:

Infliximab is effective in the treatment of Crohn disease and ulcerative colitis in children and adolescents up to week 22.
A blooming jellyfish in the northeast Atlantic and Mediterranean
Authors: Licandro P. , Conway D. V. P. , Daly Yahia M. N. , Fernandez de Puelles M. L. , Gasparini S. , Hecq J. H. , Tranter P. , Kirby R. R.
Published: April 2010

A long-term time series of plankton records collected by the continuous plankton recorder (CPR) Survey in the northeast Atlantic indicates an increased occurrence of Cnidaria since 2002. In the years 2007 and 2008, outbreaks of the warm-temperate scyphomedusa,
Pelagia noctiluca
, appeared in CPR samples between 45° N to 58° N and 1° W to 26° W. Knowing the biology of this species and its occurrence in the adjacent Mediterranean Sea, we suggest that
P. noctiluca
may be exploiting recent hydroclimatic changes in the northeast Atlantic to increase its extent and intensity of outbreaks. In pelagic ecosystems, Cnidaria can affect fish recruitment negatively. Since
P. noctiluca
is a highly venomous species, outbreaks can also be detrimental to aquaculture and make bathing waters unusable, thus having profound ecological and socio-economic consequences.
Non-climatic thermal adaptation: implications for species' responses to climate warming
Authors: Marshall David J. , McQuaid Christopher D. , Williams Gray A.
Published: April 2010

There is considerable interest in understanding how ectothermic animals may physiologically and behaviourally buffer the effects of climate warming. Much less consideration is being given to how organisms might adapt to non-climatic heat sources in ways that could confound predictions for responses of species and communities to climate warming. Although adaptation to non-climatic heat sources (solar and geothermal) seems likely in some marine species, climate warming predictions for marine ectotherms are largely based on adaptation to climatically relevant heat sources (air or surface sea water temperature). Here, we show that non-climatic solar heating underlies thermal resistance adaptation in a rocky–eulittoral-fringe snail. Comparisons of the maximum temperatures of the air, the snail's body and the rock substratum with solar irradiance and physiological performance show that the highest body temperature is primarily controlled by solar heating and re-radiation, and that the snail's upper lethal temperature exceeds the highest climatically relevant regional air temperature by approximately 22°C. Non-climatic thermal adaptation probably features widely among marine and terrestrial ectotherms and because it could enable species to tolerate climatic rises in air temperature, it deserves more consideration in general and for inclusion into climate warming models.
Reducing number entry errors: solving a widespread, serious problem
Authors: Thimbleby Harold , Cairns Paul
Published: April 2010

Number entry is ubiquitous: it is required in many fields including science, healthcare, education, government, mathematics and finance. People entering numbers are to be expected to make errors, but shockingly few systems make any effort to detect, block or otherwise manage errors. Worse, errors may be ignored but processed in arbitrary ways, with unintended results. A standard class of error (defined in the paper) is an ‘out by 10 error’, which is easily made by miskeying a decimal point or a zero. In safety-critical domains, such as drug delivery, out by 10 errors generally have adverse consequences. Here, we expose the extent of the problem of numeric errors in a very wide range of systems. An analysis of better error management is presented: under reasonable assumptions, we show that the probability of out by 10 errors can be halved by better user interface design. We provide a demonstration user interface to show that the approach is practical.

To kill an error is as good a service as, and sometimes even better than, the establishing of a new truth or fact.

(Charles
Darwin 1879 [2008]
, p. 229)
Period doubling and chaotic transient in a model of chain-branching combustion wave propagation
Authors: Gubernov Vladimir , Kolobov Andrei , Polezhaev Andrei , Sidhu Harvinder , Mercer Geoffry
Published: April 2010

The propagation of planar combustion waves in an adiabatic model with two-step chain-branching reaction mechanism is investigated. The travelling combustion wave becomes unstable with respect to pulsating perturbations as the critical parameter values for the Hopf bifurcation are crossed in the parameter space. The Hopf bifurcation is demonstrated to be of a supercritical nature and it gives rise to periodic pulsating combustion waves as the neutral stability boundary is crossed. The increase of the ambient temperature is found to have a stabilizing effect on the propagation of the combustion waves. However, it does not qualitatively change the behaviour of the travelling combustion waves. Further increase of the bifurcation parameter leads to the period-doubling bifurcation cascade and a chaotic regime of combustion wave propagation. The chaotic regime has a transient nature and the combustion wave extinguishes when the bifurcation parameter becomes sufficiently large. For Lewis numbers of fuel close to unity, the parameter regions where pulsating solutions exist become very close to each other and this makes it difficult to experimentally observe the period-doubling. It is shown that the average velocity of pulsating waves is less than the speed of the travelling wave for the same parameter values.
Quasi-steady-state and steady-state models for heat and moisture transport in textile assemblies
Authors: Ye C. , Li B. , Sun W.
Published: April 2010

Heat and moisture transport plays an important role in many engineering areas. In many sweat transport systems, such as clothing assembly, the moisture concentration (or sweat) is relative small and the air concentration reaches a steady state quickly. In this paper, a quasi-steady-state multi-component and multi-phase model for heat and moisture transport in porous textile materials with phase change is proposed. An analytic form of the air concentration is obtained in terms of the mixture gas (vapour and air) concentration and temperature. The new model is described in the form of a single-component flow with an extra air resistance (permeability), involving only the vapour concentration (or pressure), temperature and water content. The existence of the classical positive solutions of the corresponding steady-state model is proved. Two types of clothing assemblies are investigated numerically. The comparisons among the experimental measurements and numerical results of the fully dynamic model, the proposed quasi-steady-state model and steady-state model are also presented. Numerical results show that the proposed quasi-steady-state model is realistic and less complicated.
Phylogenetic diversity does not capture body size variation at risk in the world's mammals
Authors: Fritz Susanne A. , Purvis Andy
Published: April 2010

Mammals contribute to important ecosystem processes and services, but many mammalian species are threatened with extinction. We compare how global patterns in three measures of mammalian diversity—species richness, phylogenetic diversity (PD) and body mass variance (BMV)—would change if all currently threatened species were lost. Given that many facets of species' ecology and life history scale predictably with body mass, the BMV in a region roughly reflects the diversity of species' roles within ecosystems and so is a simple proxy for functional diversity (FD). PD is also often considered to be a proxy for FD, but our results suggest that BMV losses within ecoregions would be much more severe than losses of PD or species richness, and that its congruence with the latter two measures is low. Because of the disproportionate loss of large mammals, 65 per cent of ecoregions would lose significantly more BMV than under random extinction, while only 11 per cent would lose significantly more PD. Ecosystem consequences of these selective losses may be profound, especially throughout the tropics, but are not captured by PD. This low surrogacy stresses a need for conservation prioritization based on threatened trait diversity, and for conservation efforts to take an ecosystem perspective.
The shape and tempo of language evolution
Authors: Greenhill S. J. , Atkinson Q. D. , Meade A. , Gray R. D.
Published: April 2010

There are approximately 7000 languages spoken in the world today. This diversity reflects the legacy of thousands of years of cultural evolution. How far back we can trace this history depends largely on the rate at which the different components of language evolve. Rates of lexical evolution are widely thought to impose an upper limit of 6000–10 000 years on reliably identifying language relationships. In contrast, it has been argued that certain structural elements of language are much more stable. Just as biologists use highly conserved genes to uncover the deepest branches in the tree of life, highly stable linguistic features hold the promise of identifying deep relationships between the world's languages. Here, we present the first global network of languages based on this typological information. We evaluate the relative evolutionary rates of both typological and lexical features in the Austronesian and Indo-European language families. The first indications are that typological features evolve at similar rates to basic vocabulary but their evolution is substantially less tree-like. Our results suggest that, while rates of vocabulary change are correlated between the two language families, the rates of evolution of typological features and structural subtypes show no consistent relationship across families.
Incentives and opportunism: from the carrot to the stick
Authors: Hilbe Christian , Sigmund Karl
Published: April 2010

Cooperation in public good games is greatly promoted by positive and negative incentives. In this paper, we use evolutionary game dynamics to study the evolution of opportunism (the readiness to be swayed by incentives) and the evolution of trust (the propensity to cooperate in the absence of information on the co-players). If both positive and negative incentives are available, evolution leads to a population where defectors are punished and players cooperate, except when they can get away with defection. Rewarding behaviour does not become fixed, but can play an essential role in catalysing the emergence of cooperation, especially if the information level is low.
Adaptive dynamics of cooperation may prevent the coexistence of defectors and cooperators and even cause extinction
Authors: Parvinen Kalle
Published: April 2010

It has recently been demonstrated that ecological feedback mechanisms can facilitate the emergence and maintenance of cooperation in public goods interactions: the replicator dynamics of defectors and cooperators can result, for example, in the ecological coexistence of cooperators and defectors. Here we show that these results change dramatically if cooperation strategy is not fixed but instead is a continuously varying trait under natural selection. For low values of the factor with which the value of resources is multiplied before they are shared among all participants, evolution will always favour lower cooperation strategies until the population falls below an Allee threshold and goes extinct, thus evolutionary suicide occurs. For higher values of the factor, there exists a unique evolutionarily singular strategy, which is convergence stable. Because the fitness function is linear with respect to the strategy of the mutant, this singular strategy is neutral against mutant invasions. This neutrality disappears if a nonlinear functional response in receiving benefits is assumed. For strictly concave functional responses, singular strategies become uninvadable. Evolutionary branching, which could result in the evolutionary emergence of cooperators and defectors, can occur only with locally convex functional responses, but we illustrate that it can also result in coevolutionary extinction.