bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Noise Suppression on Intelligibility: Experts' Opinions and Naïve Normal-Hearing Listeners' Performance
Authors: Hilkhuysen Gaston L. M. , Gaubitch Nikolay , Huckvale Mark
Published: October 2012

Purpose

In this study, the authors investigated how well experts can adjust the settings of a commercial noise-reduction system to optimize the intelligibility for naive normal-hearing listeners.

Method

In Experiment 1, 5 experts adjusted parameters for a noise-reduction system while aiming to optimize intelligibility. The stimuli consisted of speech presented in car-cabin noise or babble at 5 different signal-to-noise ratios (SNRs). In Experiment 2, the effects of processing with these settings were measured with 10 listeners undertaking an intelligibility test. In Experiment 3, the intelligibility of a broad range of settings was investigated with another 10 listeners to determine whether the experts' chosen settings could have been improved.

Results

Low Cronbach's alphas indicated that parameter settings varied considerably within and across experts. For very low SNRs, mean proposed settings differed from those for higher SNRs. The different settings had no significant effects on intelligibility for naive normal-hearing listeners. At high SNRs, the settings proposed by experts were found to deteriorate intelligibility. Superior intelligibility for naive normal-hearing listeners was achievable from settings other than the ones proposed by the experts.

Conclusion

While attempting to enhance noisy speech, experts may propose settings that deteriorate intelligibility for naive normal-hearing listeners.
Direct One-Pot Cobalt(II) Phthalocyanine Catalyzed Synthesis of N-Substituted Isoindolinones
Authors: Kumar Vishal , Sharma Upendra , Singh Bikram , Kumar Neeraj
Published: October 2012

A direct one-pot synthetic approach is described wherein cobalt(ii) phthalocyanine (CoPc) catalyzed reductive amination of 2-carboxybenzaldehyde, followed by intramolecular amidation afforded N-substituted isoindolinones. The method used diphenylsilane as reducing agent in ethanol. High chemoselectivity with excellent yield was obtained in most of the studied substrates.
HIV-1 Nef interferes with T-lymphocyte circulation through confined environments in vivo
Authors: Stolp Bettina , Imle Andrea , Coelho Fernanda Matos , Hons Miroslav , Gorina Roser , Lyck Ruth , Stein Jens V. , Fackler Oliver T.
Published: October 2012

HIV-1 negative factor (Nef) elevates virus replication and contributes to immune evasion in vivo. As one of its established in vitro activities, Nef interferes with T-lymphocyte chemotaxis by reducing host cell actin dynamics. To explore Nef’s influence on in vivo recirculation of T lymphocytes, we assessed lymph-node homing of Nef-expressing primary murine lymphocytes and found a drastic impairment in homing to peripheral lymph nodes. Intravital imaging and 3D immunofluorescence reconstruction of lymph nodes revealed that Nef potently impaired T-lymphocyte extravasation through high endothelial venules and reduced subsequent parenchymal motility. Ex vivo analyses of transendothelial migration revealed that Nef disrupted T-lymphocyte polarization and interfered with diapedesis and migration in the narrow subendothelial space. Consistently, Nef specifically affected T-lymphocyte motility modes used in dense environments that pose high physical barriers to migration. Mechanistically, inhibition of lymph node homing, subendothelial migration and cell polarization, but not diapedesis, depended on Nef’s ability to inhibit host cell actin remodeling. Nef-mediated interference with in vivo recirculation of T lymphocytes may compromise T-cell help and thus represents an important mechanism for its function as a HIV pathogenicity factor.
Early Solar System hydrothermal activity in chondritic asteroids on 1–10-year timescales
Authors: Dyl Kathryn A. , Bischoff Addi , Ziegler Karen , Young Edward D. , Wimmer Karl , Bland Phil A.
Published: October 2012

Chondritic meteorites are considered the most primitive remnants of planetesimals from the early Solar System. As undifferentiated objects, they also display widespread evidence of water–rock interaction on the parent body. Understanding this history has implications for the formation of planetary bodies, the delivery of water to the inner Solar System, and the formation of prebiotic molecules. The timescales of water–rock reactions in these early objects, however, are largely unknown. Here, we report evidence for short-lived water–rock reactions in the highly metamorphosed ordinary chondrite breccia Villalbeto de la Peña (L6). An exotic clast (
d
= 2cm) has coexisting variations in feldspar composition and oxygen isotope ratios that can only result from hydrothermal conditions. The profiles were modeled at
T
= 800 °C and
P
(H
2
O) = 1 bar using modified grain-boundary diffusion parameters for oxygen self-diffusion and reaction rates of NaSiCa
-1
Al
-1
exchange in a fumarole. The geochemical data are consistent with hydrothermal activity on the parent body lasting only 1–10 y. This result has wide-ranging implications for the geological history of chondritic asteroids.
Phase competition in trisected superconducting dome
Authors: Vishik I. M. , Hashimoto M. , He Rui-Hua , Lee Wei-Sheng , Schmitt Felix , Lu Donghui , Moore R. G. , Zhang C. , Meevasana W. , Sasagawa T. , Uchida S. , Fujita Kazuhiro , Ishida S. , Ishikado M. , Yoshida Yoshiyuki , Eisaki Hiroshi , Hussain Zahid , Devereaux Thomas P. , Shen Zhi-Xun
Published: October 2012

A detailed phenomenology of low energy excitations is a crucial starting point for microscopic understanding of complex materials, such as the cuprate high-temperature superconductors. Because of its unique momentum-space discrimination, angle-resolved photoemission spectroscopy (ARPES) is ideally suited for this task in the cuprates, where emergent phases, particularly superconductivity and the pseudogap, have anisotropic gap structure in momentum space. We present a comprehensive doping- and temperature-dependence ARPES study of spectral gaps in Bi
2
Sr
2
CaCu
2
O

8+
δ

, covering much of the superconducting portion of the phase diagram. In the ground state, abrupt changes in near-nodal gap phenomenology give spectroscopic evidence for two potential quantum critical points,
p
= 0.19 for the pseudogap phase and
p
= 0.076 for another competing phase. Temperature dependence reveals that the pseudogap is not static below

T
c

and exists
p >
0.19 at higher temperatures. Our data imply a revised phase diagram that reconciles conflicting reports about the endpoint of the pseudogap in the literature, incorporates phase competition between the superconducting gap and pseudogap, and highlights distinct physics at the edge of the superconducting dome.
Autophagy protects against active tuberculosis by suppressing bacterial burden and inflammation
Authors: Castillo Eliseo F. , Dekonenko Alexander , Arko-Mensah John , Mandell Michael A. , Dupont Nicolas , Jiang Shanya , Delgado-Vargas Monica , Timmins Graham S. , Bhattacharya Dhruva , Yang Hongliang , Hutt Julie , Lyons C. Rick , Dobos Karen M. , Deretic Vojo
Published: October 2012

Autophagy is a cell biological pathway affecting immune responses. In vitro, autophagy acts as a cell-autonomous defense against
Mycobacterium tuberculosis
, but its role in vivo is unknown. Here we show that autophagy plays a dual role against tuberculosis: antibacterial and anti-inflammatory.
M
.
tuberculosis
infection of Atg5
fl/fl
LysM-Cre
+
mice relative to autophagy-proficient littermates resulted in increased bacillary burden and excessive pulmonary inflammation characterized by neutrophil infiltration and IL-17 response with increased IL-1α levels. Macrophages from uninfected Atg5
fl/fl
LysM-Cre
+
mice displayed a cell-autonomous IL-1α hypersecretion phenotype, whereas T cells showed propensity toward IL-17 polarization during nonspecific activation or upon restimulation with mycobacterial antigens. Thus, autophagy acts in vivo by suppressing both
M
.
tuberculosis
growth and damaging inflammation.
C1q limits dendritic cell differentiation and activation by engaging LAIR-1
Authors: Son Myoungsun , Santiago-Schwarz Frances , Al-Abed Yousef , Diamond Betty
Published: October 2012

C1q, the first component of complement, and leukocyte-associated Ig-like receptor 1 (LAIR-1; CD305), an inhibitory receptor expressed on hematopoietic cells, have both been associated with arrest of monocyte-derived dendritic cell (DC) differentiation and inhibition of Toll-like receptor activity in plasmacytoid DCs. Defects in both molecules have been implicated in susceptibility to, and progression of, systemic lupus erythematosus. Inhibitory signaling partners for C1q on monocytes and DCs remain undefined. Because C1q contains collagen-like motifs and LAIR-1 is a universal collagen receptor, we hypothesized that C1q is a functional ligand for LAIR-1. Binding analyses in cell-free systems and on the cell membrane demonstrate that C1q and its collagen tail associate with LAIR-1 and LAIR-2 (CD306), a soluble inhibitor of LAIR-1. Both C1q and its collagen tail trigger phosphorylation of LAIR-1 immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in monocytes. Functional analyses show that C1q-mediated inhibition of monocyte-DC differentiation and C1q-mediated inhibition of IFN-α production by plasmacytoid DCs were both reversed by LAIR-2. Moreover, C1q-mediated inhibition of DC differentiation was reversed by LAIR-1 siRNA. Thus, C1q is a functional ligand for LAIR-1 restricting immune cell differentiation and activation. The discovery of C1q interactions with LAIR-1 and LAIR-2 lends much needed insight into molecular mechanisms operating to prevent the loss of tolerance, particularly in systemic lupus erythematosus.
Hyperactive self-inactivating
piggyBac
for transposase-enhanced pronuclear microinjection transgenesis
Authors: Marh Joel , Stoytcheva Zoia , Urschitz Johann , Sugawara Atsushi , Yamashiro Hideaki , Owens Jesse B. , Stoytchev Ilko , Pelczar Pawel , Yanagimachi Ryuzo , Moisyadi Stefan
Published: October 2012

We have developed a unique method for mouse transgenesis. The transposase-enhanced pronuclear microinjection (PNI) technique described herein uses the hyperactive
piggyBac
transposase to insert a large transgene into the mouse genome. This procedure increased transgene integration efficiency by fivefold compared with conventional PNI or intracytoplasmic sperm injection-mediated transgenesis. Our data indicate that the transposase-enhanced PNI technique additionally requires fewer embryos to be microinjected than traditional methods to obtain transgenic animals. This transposase-mediated approach is also very efficient for single-cell embryo cytoplasmic injections, offering an easy-to-implement transgenesis method to the scientific community.
Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation
Authors: Beshiri Michael L. , Holmes Katherine B. , Richter William F. , Hess Samuel , Islam Abul B. M. M. K. , Yan Qin , Plante Lydia , Litovchick Larisa , Gévry Nicolas , Lopez-Bigas Nuria , Kaelin William G. , Benevolenskaya Elizaveta V.
Published: October 2012

Epigenetic regulation underlies the robust changes in gene expression that occur during development. How precisely epigenetic enzymes contribute to development and differentiation processes is largely unclear. Here we show that one of the enzymes that removes the activating epigenetic mark of trimethylated lysine 4 on histone H3, lysine (K)-specific demethylase 5A (KDM5A), reinforces the effects of the retinoblastoma (RB) family of transcriptional repressors on differentiation. Global location analysis showed that KDM5A cooccupies a substantial portion of target genes with the E2F4 transcription factor. During ES cell differentiation, knockout of KDM5A resulted in derepression of multiple genomic loci that are targets of KDM5A, denoting a direct regulatory function. In terminally differentiated cells, common KDM5A and E2F4 gene targets were bound by the pRB-related protein p130, a DREAM complex component. KDM5A was recruited to the transcription start site regions independently of E2F4; however, it cooperated with E2F4 to promote a state of deepened repression at cell cycle genes during differentiation. These findings reveal a critical role of H3K4 demethylation by KDM5A in the transcriptional silencing of genes that are suppressed by RB family members in differentiated cells.
Accelerative and decelerative effects of hedonic valence and emotional arousal during visual scene processing
Authors: Ihssen Niklas , Keil Andreas
Published: October 2012

Perceptual processing of natural scene pictures is enhanced when the scene conveys emotional content. Such “motivated attention” to pleasant and unpleasant pictures has been shown to improve identification accuracy in non-speeded behavioural tasks. An open question is whether emotional content also modulates the speed of visual scene processing. In the present studies we show that unpleasant content reliably slowed two-choice categorization of pictures, irrespective of physical image properties, perceptual complexity, and categorization instructions. Conversely, pleasant content did not slow or even accelerated choice reactions, relative to neutral scenes. As indicated by lateralized readiness potentials, these effects occurred at cognitive processing rather than motor preparation/execution stages. Specifically, analysis of event-related potentials showed a prolongation of early scene discrimination for stimuli perceived as emotionally arousing, regardless of valence, and reflected in delayed peaks of the N1 component. In contrast, the timing of other processing steps, reflected in the P2 and late positive potential components and presumably related to post-discriminatory processes such as stimulus–response mapping, appeared to be determined by hedonic valence, with more pleasant scenes eliciting faster processing. Consistent with this model, varying arousal (low/high) within the emotional categories mediated the effects of valence on choice reaction speed. Functionally, arousal may prolong stimulus analysis in order to prevent erroneous and potentially harmful decisions. Pleasantness may act as a safety signal allowing rapid initiation of overt responses.
TspanC8 tetraspanins regulate ADAM10/Kuzbanian trafficking and promote Notch activation in flies and mammals
Authors: Dornier Emmanuel , Coumailleau Franck , Ottavi Jean-François , Moretti Julien , Boucheix Claude , Mauduit Philippe , Schweisguth François , Rubinstein Eric
Published: October 2012

The metalloprotease ADAM10/Kuzbanian catalyzes the ligand-dependent ectodomain shedding of Notch receptors and activates Notch. Here, we show that the human tetraspanins of the evolutionary conserved TspanC8 subfamily (Tspan5, Tspan10, Tspan14, Tspan15, Tspan17, and Tspan33) directly interact with ADAM10, regulate its exit from the endoplasmic reticulum, and that four of them regulate ADAM10 surface expression levels. In an independent RNAi screen in Drosophila, two TspanC8 genes were identified as Notch regulators. Functional analysis of the three Drosophila TspanC8 genes (Tsp3A, Tsp86D, and Tsp26D) indicated that these genes act redundantly to promote Notch signaling. During oogenesis, TspanC8 genes were up-regulated in border cells and regulated Kuzbanian distribution, Notch activity, and cell migration. Furthermore, the human TspanC8 tetraspanins Tspan5 and Tspan14 positively regulated ligand-induced ADAM10-dependent Notch1 signaling. We conclude that TspanC8 tetraspanins have a conserved function in the regulation of ADAM10 trafficking and activity, thereby positively regulating Notch receptor activation.
Critical role for the kinesin KIF3A in the HIV life cycle in primary human macrophages
Authors: Gaudin Raphaël , Cunha de Alencar Bruna , Jouve Mabel , Bèrre Stefano , Le Bouder Emmanuel , Schindler Michael , Varthaman Aditi , Gobert François-Xavier , Benaroch Philippe
Published: October 2012

Macrophages are long-lived target cells for HIV infection and are considered viral reservoirs. HIV assembly in macrophages occurs in virus-containing compartments (VCCs) in which virions accumulate and are stored. The regulation of the trafficking and release of these VCCs remains unknown. Using high resolution light and electron microscopy of HIV-1–infected primary human macrophages, we show that the spatial distribution of VCCs depended on the microtubule network and that VCC-limiting membrane was closely associated with KIF3A+ microtubules. Silencing KIF3A strongly decreased virus release from HIV-1–infected macrophages, leading to VCC accumulation intracellularly. Time-lapse microscopy further suggested that VCCs and associated KIF3A move together along microtubules. Importantly, KIF3A does not play a role in HIV release from T cells that do not possess VCCs. These results reveal that HIV-1 requires the molecular motor KIF3 to complete its cycle in primary macrophages. Targeting this step may lead to novel strategies to eliminate this viral reservoir.
ProNGF, a cytokine induced after myocardial infarction in humans, targets pericytes to promote microvascular damage and activation
Authors: Siao Chia-Jen , Lorentz Christina U. , Kermani Pouneh , Marinic Tina , Carter John , McGrath Kelly , Padow Victoria A. , Mark Willie , Falcone Domenick J. , Cohen-Gould Leona , Parrish Diana C. , Habecker Beth A. , Nykjaer Anders , Ellenson Lora H. , Tessarollo Lino , Hempstead Barbara L.
Published: October 2012

Treatment of acute cardiac ischemia focuses on reestablishment of blood flow in coronary arteries. However, impaired microvascular perfusion damages peri-infarct tissue, despite arterial patency. Identification of cytokines that induce microvascular dysfunction would provide new targets to limit microvascular damage. Pro–nerve growth factor (NGF), the precursor of NGF, is a well characterized cytokine in the brain induced by injury. ProNGF activates p75 neurotrophin receptor (p75NTR) and sortilin receptors to mediate proapoptotic responses. We describe induction of proNGF by cardiomyocytes, and p75NTR in human arterioles after fatal myocardial infarction, but not with unrelated pathologies. After mouse cardiac ischemia-reperfusion (I-R) injury, rapid up-regulation of proNGF by cardiomyocytes and p75NTR by microvascular pericytes is observed. To identify proNGF actions, we generated a mouse expressing a mutant Ngf allele with impaired processing of proNGF to mature NGF. The proNGF-expressing mouse exhibits cardiac microvascular endothelial activation, a decrease in pericyte process length, and increased vascular permeability, leading to lethal cardiomyopathy in adulthood. Deletion of p75NTR in proNGF-expressing mice rescues the phenotype, confirming the importance of p75NTR-expressing pericytes in the development of microvascular injury. Furthermore, deficiency in p75NTR limits infarct size after I-R. These studies identify novel, nonneuronal actions for proNGF and suggest that proNGF represents a new target to limit microvascular dysfunction.
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript
Authors: Benelli Matteo , Pescucci Chiara , Marseglia Giuseppina , Severgnini Marco , Torricelli Francesca , Magi Alberto
Published: October 2012

Motivation: The discovery of novel gene fusions can lead to a better comprehension of cancer progression and development. The emergence of deep sequencing of trancriptome, known as RNA-seq, has opened many opportunities for the identification of this class of genomic alterations, leading to the discovery of novel chimeric transcripts in melanomas, breast cancers and lymphomas. Nowadays, few computational approaches have been developed for the detection of chimeric transcripts. Although all of these computational methods show good sensitivity, much work remains to reduce the huge number of false-positive calls that arises from this analysis.

Results: We proposed a novel computational framework, named chimEric tranScript detection algorithm (EricScript), for the identification of gene fusion products in paired-end RNA-seq data. Our simulation study on synthetic data demonstrates that EricScript enables to achieve higher sensitivity and specificity than existing methods with noticeably lower running times. We also applied our method to publicly available RNA-seq tumour datasets, and we showed its capability in rediscovering known gene fusions.

Availability: The EricScript package is freely available under GPL v3 license at http://ericscript.sourceforge.net.

Contact:  matteo.benelli@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold
Authors: Menelaou Androniki , Marchini Jonathan
Published: October 2012

Motivation: Given the current costs of next-generation sequencing, large studies carry out low-coverage sequencing followed by application of methods that leverage linkage disequilibrium to infer genotypes. We propose a novel method that assumes study samples are sequenced at low coverage and genotyped on a genome-wide microarray, as in the 1000 Genomes Project (1KGP). We assume polymorphic sites have been detected from the sequencing data and that genotype likelihoods are available at these sites. We also assume that the microarray genotypes have been phased to construct a haplotype scaffold. We then phase each polymorphic site using an MCMC algorithm that iteratively updates the unobserved alleles based on the genotype likelihoods at that site and local haplotype information. We use a multivariate normal model to capture both allele frequency and linkage disequilibrium information around each site. When sequencing data are available from trios, Mendelian transmission constraints are easily accommodated into the updates. The method is highly parallelizable, as it analyses one position at a time.

Results: We illustrate the performance of the method compared with other methods using data from Phase 1 of the 1KGP in terms of genotype accuracy, phasing accuracy and downstream imputation performance. We show that the haplotype panel we infer in African samples, which was based on a trio-phased scaffold, increases downstream imputation accuracy for rare variants (R2 increases by >0.05 for minor allele frequency <1%), and this will translate into a boost in power to detect associations. These results highlight the value of incorporating microarray genotypes when calling variants from next-generation sequence data.

Availability: The method (called MVNcall) is implemented in a C++ program and is available from http://www.stats.ox.ac.uk/∼marchini/#software.

Contact:  marchini@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Purification of Protein AP-Toxin from Arthrinium phaeospermum Causing Blight in Bambusa pervariabilis × Dendrocalamopisis grandis and Its Metabolic Effects on Four Bamboo Varieties
Authors: Li Shu-Jiang , Zhu Tian-Hui , Zhu Han-Ming-Yue , Liang Man , Qiao Tian-Min , Han Shan , Che Guan-Nan
Published: October 2012

Bambusa pervariabilis × Dendrocalamopisis grandis blight is caused by a toxin produced by the fungus Arthrinium phaeospermum. In this study, a toxin fraction (P1-2-2) with an estimated molecular mass of 31 kDa was purified from a culture filtrate of this fungus by ammonium sulfate precipitation, Sephadex G-50 gel chromatography, Q Sepharose Fast Flow anion exchange resin, and Sephadex G-75 chromatography. The N-terminal amino acid sequence (i.e., H2N-Gln-Val-Arg-Asp-Arg-Leu-Glu-Ser-Thr) determined by Edman degradation showed homology to known serine alkaline proteases. The purified protein was named AP-toxin. Effects of the purified protein toxin on total phenol, flavonoid, total nucleic acid, DNA, RNA, soluble protein, and soluble sugar content, as well as DNase and RNase activities and disease index, were analyzed in different bamboo varieties by the impregnation method. The toxin had a significant effect on each parameter tested. In addition, a significant correlation was observed among the metabolic index, treatment time, bamboo resistance, and disease index. These data suggest that AP-toxin plays an important role in mediating the phytotoxic activities of A. phaeospermum. This study also indicates that metabolic indices could reflect the resistance indices of hybrid bamboo to blight.
Sediment suppresses herbivory across a coral reef depth gradient
Authors: Goatley Christopher H. R. , Bellwood David R.
Published: October 2012

Sediments are a ubiquitous feature of all coral reefs, yet our understanding of how they affect complex ecological processes on coral reefs is limited. Sediment in algal turfs has been shown to suppress herbivory by coral reef fishes on high-sediment, low-herbivory reef flats. Here, we investigate the role of sediment in suppressing herbivory across a depth gradient (reef base, crest and flat) by observing fish feeding following benthic sediment reductions. We found that sediment suppresses herbivory across all reef zones. Even slight reductions on the reef crest, which has 35 times less sediment than the reef flat, resulted in over 1800 more herbivore bites (h
−1
m
−2
). The Acanthuridae (surgeonfishes) were responsible for over 80 per cent of all bites observed, and on the reef crest and flat took over 1500 more bites (h
−1
m
−2
) when sediment load was reduced. These findings highlight the role of natural sediment loads in shaping coral reef herbivory and suggest that changes in benthic sediment loads could directly impair reef resilience.
Climate change and elevational diversity capacity: do weedy species take up the slack?
Authors: Chown Steven L. , le Roux Peter C. , Ramaswiela Tshililo , Kalwij Jesse M. , Shaw Justine D. , McGeoch Melodie A.
Published: October 2012

Climate change leads to species range shifts and consequently to changes in diversity. For many systems, increases in diversity capacity have been forecast, with spare capacity to be taken up by a pool of weedy species moved around by humans. Few tests of this hypothesis have been undertaken, and in many temperate systems, climate change impacts may be confounded by simultaneous increases in human-related disturbance, which also promote weedy species. Areas to which weedy species are being introduced, but with little human disturbance, are therefore ideal for testing the idea. We make predictions about how such diversity capacity increases play out across elevational gradients in non-water-limited systems. Then, using modern and historical data on the elevational range of indigenous and naturalized alien vascular plant species from the relatively undisturbed sub-Antarctic Marion Island, we show that alien species have contributed significantly to filling available diversity capacity and that increases in energy availability rather than disturbance are the probable underlying cause.
Swimming like algae: biomimetic soft artificial cilia
Authors: Sareh Sina , Rossiter Jonathan , Conn Andrew , Drescher Knut , Goldstein Raymond E.
Published: October 2012

Cilia are used effectively in a wide variety of biological systems from fluid transport to thrust generation. Here, we present the design and implementation of artificial cilia, based on a biomimetic planar actuator using soft-smart materials. This actuator is modelled on the cilia movement of the algaVolvox, and represents the cilium as a piecewise constant-curvature robotic actuator that enables the subsequent direct translation of natural articulation into a multi-segment ionic polymer metal composite actuator. It is demonstrated how the combination of optimal segmentation pattern and biologically derived per-segment driving signals reproduce natural ciliary motion. The amenability of the artificial cilia to scaling is also demonstrated through the comparison of the Reynolds number achieved with that of natural cilia.
Simple robot suggests physical interlimb communication is essential for quadruped walking
Authors: Owaki Dai , Kano Takeshi , Nagasawa Ko , Tero Atsushi , Ishiguro Akio
Published: October 2012

Quadrupeds have versatile gait patterns, depending on the locomotion speed, environmental conditions and animal species. These locomotor patterns are generated via the coordination between limbs and are partly controlled by an intraspinal neural network called the central pattern generator (CPG). Although this forms the basis for current control paradigms of interlimb coordination, the mechanism responsible for interlimb coordination remains elusive. By using a minimalistic approach, we have developed a simple-structured quadruped robot, with the help of which we propose an unconventional CPG model that consists of four decoupled oscillators with only local force feedback in each leg. Our robot exhibits good adaptability to changes in weight distribution and walking speed simply by responding to local feedback, and it can mimic the walking patterns of actual quadrupeds. Our proposed CPG-based control method suggests that physical interaction between legs during movements is essential for interlimb coordination in quadruped walking.
Power-law rheology in the bulk and at the interface: quasi-properties and fractional constitutive equations
Authors: Jaishankar Aditya , McKinley Gareth H.
Published: October 2012

Consumer products, such as foods, contain numerous polymeric and particulate additives that play critical roles in maintaining their stability, quality and function. The resulting materials exhibit complex bulk and interfacial rheological responses, and often display a distinctive power-law response under standard rheometric deformations. These power laws are not conveniently described using conventional rheological models, without the introduction of a large number of relaxation modes. We present a constitutive framework using fractional derivatives to model the power-law responses often observed experimentally. We first revisit the concept of quasi-properties and their connection to the fractional Maxwell model (FMM). Using Scott-Blair's original data, we demonstrate the ability of the FMM to capture the power-law response of ‘highly anomalous’ materials. We extend the FMM to describe the viscoelastic interfaces formed by bovine serum albumin and solutions of a common food stabilizer, Acacia gum. Fractional calculus allows us to model and compactly describe the measured frequency response of these interfaces in terms of their quasi-properties. Finally, we demonstrate the predictive ability of the FMM to quantitatively capture the behaviour of complex viscoelastic interfaces by combining the measured quasi-properties with the equation of motion for a complex fluid interface to describe the damped inertio-elastic oscillations that are observed experimentally.
When can we trust our model predictions? Unearthing structural sensitivity in biological systems
Authors: Adamson M. W. , Morozov A. Yu.
Published: October 2012

It is well recognized that models in the life sciences can be sensitive to small variations in their model functions, a phenomenon known as ‘structural sensitivity’. Conventionally, modellers test for sensitivity by varying parameters for a specific formulation of the model functions, but models can show structural sensitivity to the choice of functional representations used: a particularly concerning problem when system processes are too complex, or insufficiently understood, to theoretically justify specific parameterizations. Here we propose a rigorous test for the detection of structural sensitivity in a system with respect to the local stability of equilibria, the main idea being to project infinite dimensional function space onto a finite dimensional space by considering the local properties of the model functions. As an illustrative example, we use our test to demonstrate structural sensitivity in the seminal Rosenzweig–MacArthur predator–prey model, and show that the conventional parameter-based approach can fail to do so. We also consider some implications that structural sensitivity has for ecological modelling: we argue that when the model exhibits structural sensitivity but experimental results remain consistent it may indicate that there is a problem with the model construction, and that in some cases trying to find an ‘optimal’ parameterization of a model function may simply be impossible when the model exhibits structural sensitivity. Finally, we suggest that the phenomenon of structural sensitivity in biological models may help explain the irregular oscillations often observed in real ecosystems.
Offspring social network structure predicts fitness in families
Authors: Royle Nick J. , Pike Thomas W. , Heeb Philipp , Richner Heinz , Kölliker Mathias
Published: October 2012

Social structures such as families emerge as outcomes of behavioural interactions among individuals, and can evolve over time if families with particular types of social structures tend to leave more individuals in subsequent generations. The social behaviour of interacting individuals is typically analysed as a series of multiple dyadic (pair-wise) interactions, rather than a network of interactions among multiple individuals. However, in species where parents feed dependant young, interactions within families nearly always involve more than two individuals simultaneously. Such social networks of interactions at least partly reflect conflicts of interest over the provision of costly parental investment. Consequently, variation in family network structure reflects variation in how conflicts of interest are resolved among family members. Despite its importance in understanding the evolution of emergent properties of social organization such as family life and cooperation, nothing is currently known about how selection acts on the structure of social networks. Here, we show that the social network structure of broods of begging nestling great tits
Parus major
predicts fitness in families. Although selection at the level of the individual favours large nestlings, selection at the level of the kin-group primarily favours families that resolve conflicts most effectively.
A congruent phylogenomic signal places eukaryotes within the Archaea
Authors: Williams Tom A. , Foster Peter G. , Nye Tom M. W. , Cox Cymon J. , Embley T. Martin
Published: October 2012

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes
within
the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
Quantifying temporal change in biodiversity: challenges and opportunities
Authors: Dornelas Maria , Magurran Anne E. , Buckland Stephen T. , Chao Anne , Chazdon Robin L. , Colwell Robert K. , Curtis Tom , Gaston Kevin J. , Gotelli Nicholas J. , Kosnik Matthew A. , McGill Brian , McCune Jenny L. , Morlon Hélène , Mumby Peter J. , Øvreås Lise , Studeny Angelika , Vellend Mark
Published: October 2012

Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.
Experimental evidence for adaptive personalities in a wild passerine bird
Authors: Nicolaus Marion , Tinbergen Joost M. , Bouwman Karen M. , Michler Stephanie P. M. , Ubels Richard , Both Christiaan , Kempenaers Bart , Dingemanse Niels J.
Published: October 2012

Individuals of the same species differ consistently in risky actions. Such ‘animal personality’ variation is intriguing because behavioural flexibility is often assumed to be the norm. Recent theory predicts that between-individual differences in propensity to take risks should evolve if individuals differ in future fitness expectations: individuals with high long-term fitness expectations (i.e. that have much to lose) should behave consistently more cautious than individuals with lower expectations. Consequently, any manipulation of future fitness expectations should result in within-individual changes in risky behaviour in the direction predicted by this adaptive theory. We tested this prediction and confirmed experimentally that individuals indeed adjust their ‘exploration behaviour’, a proxy for risk-taking behaviour, to their future fitness expectations. We show for wild great tits (
Parus major
) that individuals with experimentally decreased survival probability become faster explorers (i.e. increase risk-taking behaviour) compared to individuals with increased survival probability. We also show, using quantitative genetics approaches, that non-genetic effects (i.e. permanent environment effects) underpin adaptive personality variation in this species. This study thereby confirms a key prediction of adaptive personality theory based on life-history trade-offs, and implies that selection may indeed favour the evolution of personalities in situations where individuals differ in future fitness expectations.
Traits, trees and taxa: global dimensions of biodiversity in mammals
Authors: Huang Shan , Stephens Patrick R. , Gittleman John L.
Published: October 2012

Measures of biodiversity encompass variation along several dimensions such as species richness (SR), phylogenetic diversity (PD) and functional/trait diversity (TD). At the global scale, it is widely recognized that SR and PD are strongly correlated, but the extent to which either tends to capture variation in TD is unclear. Here, we assess relationships among PD, SR and TD for a number of traits both across clades and regional assemblages of mammals. We also contrast results using two different measures of TD, trait variance and a new measure we refer to as trait bin filling (the number of orders of magnitude of variation that contain at least one species). When TD is defined as trait variance, PD is a much stronger correlate of TD than SR across clades, consistent with hypotheses about the conservation value of PD. However, when TD is defined as bin filling, PD and SR show similar correlations with TD across clades and space. We also investigate potential losses of SR, PD and TD if species that are currently threatened were to go extinct, and find that threatened PD is often a similar predictor of threatened TD as SR.
Understanding specialism when the jack of all trades can be the master of all
Authors: Remold Susanna
Published: October 2012

Specialism is widespread in nature, generating and maintaining diversity, but recent work has demonstrated that generalists can be equally fit as specialists in some shared environments. This no-cost generalism challenges the maxim that ‘the jack of all trades is the master of none’, and requires evolutionary genetic mechanisms explaining the existence of specialism and no-cost generalism, and the persistence of specialism in the face of selection for generalism. Examining three well-described mechanisms with respect to epistasis and pleiotropy indicates that sign (or antagonistic) pleiotropy without epistasis cannot explain no-cost generalism and that magnitude pleiotropy without epistasis (including directional selection and mutation accumulation) cannot explain the persistence of specialism. However, pleiotropy with epistasis can explain all. Furthermore, epistatic pleiotropy may allow past habitat use to influence future use of novel environments, thereby affecting disease emergence and populations' responses to habitat change.
Continent-wide tracking to determine migratory connectivity and tropical habitat associations of a declining aerial insectivore
Authors: Fraser Kevin C. , Stutchbury Bridget J. M. , Silverio Cassandra , Kramer Patrick M. , Barrow John , Newstead David , Mickle Nanette , Cousens Bruce F. , Lee J. Charlene , Morrison Danielle M. , Shaheen Tim , Mammenga Paul , Applegate Kelly , Tautin John
Published: October 2012

North American birds that feed on flying insects are experiencing steep population declines, particularly long-distance migratory populations in the northern breeding range. We determine, for the first time, the level of migratory connectivity across the range of a songbird using direct tracking of individuals, and test whether declining northern populations have higher exposure to agricultural landscapes at their non-breeding grounds in South America. We used light-level geolocators to track purple martins,
Progne subis
, originating from North American breeding populations, coast-to-coast (
n
= 95 individuals). We show that breeding populations of the eastern subspecies,
P. s. subis
, that are separated by
ca
. 2000 km, nevertheless have almost completely overlapping non-breeding ranges in Brazil. Most (76%)
P. s. subis
overwintered in northern Brazil near the Amazon River, not in the agricultural landscape of southern Brazil. Individual non-breeding sites had an average of 91 per cent forest and only 4 per cent agricultural ground cover within a 50 km radius, and birds originating from declining northern breeding populations were not more exposed to agricultural landscapes than stable southern breeding populations. Our results show that differences in wintering location and habitat do not explain recent trends in breeding population declines in this species, and instead northern populations may be constrained in their ability to respond to climate change.
Energy-Dominated Local Carbon Emissions in Beijing 2007: Inventory and Input-Output Analysis
Authors: Guo Shan , Liu J. B. , Shao Ling , Li J. S. , An Y. R.
Published: October 2012

For greenhouse gas (GHG) emissions by Beijing economy 2007, a concrete emission inventory covering carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) is presented and associated with an input-output analysis to reveal the local GHG embodiment in final demand and trade without regard to imported emissions. The total direct GHG emissions amount to 1.06E + 08 t CO2-eq, of which energy-related CO2emissions comprise 90.49%, non-energy-related CO2emissions 6.35%, CH4emissions 2.33%, and N2O emissions 0.83%, respectively. In terms of energy-related CO2emissions, the largest source is coal with a percentage of 53.08%, followed by coke with 10.75% and kerosene with 8.44%. Sector 26 (Construction Industry) holds the top local emissions embodied in final demand of 1.86E + 07 t CO2-eq due to its considerable capital, followed by energy-intensive Sectors 27 (Transport and Storage) and 14 (Smelting and Pressing of Ferrous and Nonferrous Metals). The GHG emissions embodied in Beijing's exports are 4.90E + 07 t CO2-eq, accounting for 46.01% of the total emissions embodied in final demand. The sound scientific database totally based on local emissions is an important basis to make effective environment and energy policies for local decision makers.
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
Authors: Schadt Eric E. , Banerjee Onureena , Fang Gang , Feng Zhixing , Wong Wing H. , Zhang Xuegong , Kislyuk Andrey , Clark Tyson A. , Luong Khai , Keren-Paz Alona , Chess Andrew , Kumar Vipin , Chen-Plotkin Alice , Sondheimer Neal , Korlach Jonas , Kasarskis Andrew
Published: October 2012

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.