bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal induced inhomogeneous Schottky barrier height in AlGaN/GaN Schottky diode
Authors: Shin Jong-Hoon , Park Jinhong , Jang SeungYup , Jang T. , Sang Kim Kyu
Published: June 2013

The dependence of barrier height inhomogeneity on the gate metal has been investigated for the AlGaN/GaN Schottky diode. The analysis from the electroreflectance spectroscopy measurement for different types of Schottky gate metals tried (in this case, Au, Pt, Pd, and Ni) reveals that the surface donor states of AlGaN/GaN heterostructure strongly depends on the type of Schottky gate metals used, which suggests that barrier height inhomogeneity is strongly dependent on the gate metal. The X-ray photoelectron spectroscopy also reveals a strong correlation between the barrier height inhomogeneity and the gate metal type.
Radiation from charges in the continuum limit
Authors: Ianconescu Reuven
Published: June 2013

It is known that an accelerating charge radiates according to Larmor formula. On the other hand, any DC current following a curvilinear path, consists of accelerating charges, but in such case the radiated power is 0. The scope of this paper is to analyze and quantify how a system of charges goes from a radiating state to a non radiating state when the charges distribution goes to the continuum limit. Understanding this is important from the theoretical point of view and the results of this work are applicable to particle accelerator, cyclotron and other high energy devices.
Anomalous optical phonons in Cs0.9(NH4)0.1H2AsO4: A temperature-dependent Raman Study
Authors: Kumar P. , Sriprakash G. , Rukmani K. , Ramesh K. P. , Muthu D. V. S.
Published: June 2013

We determine the nature of coupled phonons in mixed crystal of Cs0.9(NH4)0.1H2AsO4 using inelastic light scattering studies in the temperature range of 5 K to 300 K covering a spectral range of 60–1100 cm−1. The phase transition in this system are marked by the splitting of phonon modes, appearance of new modes and anomalies in the frequency as well as linewidth of the phonon modes near transition temperature. In particular, we observed the splitting of symmetric (v1) and antisymmetric (v3) stretching vibrations associated with AsO4 tetrahedra below transition temperature ($T_c^*$Tc* ∼ 110 K) attributed to the lowering of site symmetry of AsO4 in orthorhombic phase below transition temperature. In addition, the step-up (hardening) and step-down (softening) of the AsO4 bending vibrations (v4 (S9, S11) and v2 (S6)) below transition temperature signals the rapid development of long range ferroelectric order and proton ordering. The lowest frequency phonon (S1) mode observed at ∼92 cm−1 shows anomalous blue shift (∼12 %) from 300 K to 5 K with no sharp transition near $T_c^*$Tc* unlike other observed phonon modes signaling its potential coupling with the proton tunneling mode.
Expanded use of sense codons is regulated by modified cytidines in tRNA
Authors: Cantara William A. , Murphy Frank V. , Demirci Hasan , Agris Paul F.
Published: June 2013

Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNA
Met
. This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f
5
C), at the wobble position-34 of human mitochondrial

(

) enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon•anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson–Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f
5
C
34
•A base pair geometry with two hydrogen bonds.
Activation and dynamic network of the M2 muscarinic receptor
Authors: Miao Yinglong , Nichols Sara E. , Gasper Paul M. , Metzger Vincent T. , McCammon J. Andrew
Published: June 2013

G-protein-coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. Although significant advances have been made in structural studies of GPCRs, details of their activation mechanism remain unclear. The X-ray crystal structure of the M2 muscarinic receptor, a key GPCR that regulates human heart rate and contractile forces of cardiomyocytes, was determined recently in an inactive antagonist-bound state. Here, activation of the M2 receptor is directly observed via accelerated molecular dynamics simulation, in contrast to previous microsecond-timescale conventional molecular dynamics simulations in which the receptor remained inactive. Receptor activation is characterized by formation of a Tyr2065.58–Tyr4407.53hydrogen bond and ∼6-Å outward tilting of the cytoplasmic end of transmembrane α-helix 6, preceded by relocation of Trp4006.48toward Phe1955.47and Val1995.51and flipping of Tyr4307.43away from the ligand-binding cavity. Network analysis reveals that communication in the intracellular domains is greatly weakened during activation of the receptor. Together with the finding that residue motions in the ligand-binding and G-protein-coupling sites of the apo receptor are correlated, this result highlights a dynamic network for allosteric regulation of the M2 receptor activation.
A note on sheaves without self-extensions on the projective 𝑛-space
Authors: Happel Dieter , Zacharia Dan
Published: June 2013

Let

P

n

\textbf {P}^n

be the projective

n
n

-space over the complex numbers. In this note we show that an indecomposable rigid coherent sheaf on

P

n

\textbf {P}^n

has a trivial endomorphism algebra. This generalizes a result of Drézet for

n
=
2.

n=2.
Recovery of Resistant Starch by a Classical and a New Assay for Dietary Fiber
Authors: Maningat Clodualdo C. , Seib Paul A. , Bassi Sukh D.
Published: June 2013

In vitro assays of dietary fiber, which include enzymatic removal of starch and protein from a sample, give variable recovery of the resistant starch fraction, depending on the class of resistant starch and its resilience to different amylolytic conditions. This paper summarizes our views and opinions on the classical and the new assay for dietary fiber.
Hepatitis C virus/human interactome identifies SMURF2 and the viral protease as critical elements for the control of TGF‐β signaling
Authors: Verga‐Gérard Amandine , Porcherot Marine , Meyniel‐Schicklin Laurène , André Patrice , Lotteau Vincent , Perrin‐Cocon Laure
Published: June 2013

TGF‐β signaling induces epithelial to mesenchymal transition (EMT) and plays an important role in hepatocellular carcinoma (HCC) development. Clinical observations indicate that hepatitis C virus (HCV) chronic infection, which is a major cause of HCC, induces TGF‐β signaling perturbations. Here, we investigate the mechanisms by which HCV nonstructural proteins interfere with TGF‐β signaling, in human hepatoma cell lines expressing HCV subgenomic replicon. A transcriptomic study showed that TGF‐β stimulation of these cells resulted in a protumoral gene expression profile and in up‐regulation of EMT‐related genes compared to control interferon‐treated cells not expressing HCV proteins. We found that the viral protease NS3‐4A interacted with SMURF2, a negative regulator of TGF‐β signaling. In cells expressing HCV subgenomic replicon or NS3‐4A, TGF‐β stimulation induced an increased expression of SMAD‐dependent genes compared to control cells. This enhanced signaling was suppressed by SMURF2 overexpression and mimicked by SMURF2 silencing. In addition, NS3‐4A expression resulted in an increased and prolonged TGF‐β‐induced phosphorylation of SMAD2/3 that was abrogated by SMURF2 overexpression. Neither NS3‐4A protease activity nor SMURF2 ubiquitin‐ligase activity was required to affect TGF‐β signaling. Therefore, by targeting SMURF2, NS3‐4A appears to block the negative regulation of TGF‐β signaling, increasing the responsiveness of cells to TGF‐β. Verga‐Gérard, A., Porcherot, M., Meyniel‐Schicklin, L., André, P., Lotteau, V, and Perrin‐Cocon, L. Hepatitis C virus/human interactome identifies SMURF2 and the viral protease as critical elements for the control of TGF‐β signaling. FASEB J. 27, 4027–4040 (2013). www.fasebj.org
Essential Role of Angiotensin Receptors in the Modulation of Intestinal Epithelial Cell Apoptosis
Authors: Wang Wensheng , Sun Lihua , Xiao Weidong , Yang Hua
Published: June 2013

Background and Aim:

We have previously shown that angiotensin II (ANGII) plays an important role in the regulation of the apoptosis of intestinal epithelial cells (IECs). In this study, we investigated the pathway by which ANGII modulates apoptosis of the IECs.

Methods:

Epithelial cells (HT‐29) were cultured; the ANGII receptor type‐1 (AT1R) inhibitor (Losartan) and ANGII receptor type‐2 (AT2R) inhibitor (PD123319) were used separately to block the ANGII receptor. Flow cytometry was used to detect the apoptosis of the IECs. In the in vivo study, Sprague‐Dawley rats were divided into 4 groups: sham group, which received a ileum transection (n = 6); sham + angiotensin‐converting enzyme inhibitor (ACE‐I) group, which received a ileum transection, and lavage with ACE‐I (enalaprilat 2 mg · kg−1 day−1) (n = 6); short bowel syndrome (SBS) group, which received a 70% mid‐intestinal resection (n = 6); and SBS + ACE‐I group, which received a 70% mid‐intestinal resection, and lavage with enalaprilat (2 mg · kg−1 day−1) (n = 6). Sampling was done 10 days after surgery. The expression of ANGII receptors Bax and Bcl‐2 was detected with immunofluorescence, real‐time‐polymerase chain reaction, and Western blot methods.

Results:

Massive small bowel resection led to a significant increase in epithelial cells apoptosis, and the addition of ACE‐I to SBS rat significantly attenuated this increase in apoptosis. AT1R expression on intestinal mucosa surface decreased after small bowel resection. Pretreatment with the AT1R antagonist Losartan significantly attenuated the increase of epithelial cell apoptosis caused by ANGII administration. Moreover, the Bcl‐2/Bax ratio was found to be increased in cells pretreated with Losartan, which indicates a proapoptotic role of AT1R in cultured HT‐29 cell lines.

Conclusions:

These findings suggest that ANGII plays an important role in the regulation of apoptosis of the IECs. AT1R may be of crucial importance for the modulation of intestinal EC apoptosis.
Are Thiopurines Always Contraindicated After Thiopurine‐Induced Pancreatitis in Inflammatory Bowel Disease?
Authors: Ledder Oren D. , Lemberg Daniel A. , Ooi Chee Y. , Day Andrew S.
Published: June 2013

Background and Aims:

Thiopurine use in inflammatory bowel disease (IBD) is well established for maintenance of disease remission. Approximately 3% of patients with IBD develop thiopurine‐induced pancreatitis (TIP) as an idiosyncratic reaction. Patients diagnosed as having TIP are largely considered not to be candidates for future use of this drug. We hypothesize that previous TIP is not an absolute contraindication to retrialing a different thiopurine.

Methods:

This case series is a retrospective chart review of those patients with IBD in whom thiopurines were successfully reintroduced following suspected TIP. The patients were all cared for in 2 Australasian pediatric IBD services. Four cases are presented of TIP appropriately related temporally to azathioprine commencement, with no other apparent cause of pancreatitis identified. All of these patients were trialled on 6‐mercaptopurine according to clinical need and this was well tolerated in all cases.

Results and Conclusions:

This report is the largest case series to date focusing on the reintroduction of a thiopurine following suspected thiopurine induced pancreatitis. All of the patients had a typical presentation of TIP. This case series should call into question the assumption that suspected TIP is an absolute contraindication for the future use of this class of drug. Cautious reintroduction of a thiopurine, in a controlled setting, should be considered in certain circumstances. The clinical relevance of this option is most marked in patients with complicated disease requiring long‐term immunosuppression, in whom other therapies are poorly tolerated or contraindicated.
Protozoa as a Cause of Recurrent Abdominal Pain in Children
Authors: Gijsbers Carolien F.M. , Schweizer Joachim J. , Büller Hans A.
Published: June 2013

Objectives:

The aim of this study was to investigate whether protozoa can be identified as a cause of recurrent abdominal pain (RAP), and whether protozoan infections can be recognized by a specific clinical presentation.

Methods:

For 2 years, all patients (ages 4–16 years) fulfilling the Apley criteria of RAP referred to secondary care were prospectively evaluated for protozoa (Giardia lamblia, Dientamoeba fragilis, Blastocystis hominis) and treated if positive. Re‐examination followed at least 10 days after treatment. Disappearance of pain with eradication and a pain‐free follow‐up of at least 6 months were considered to be indicative of a causal relation with RAP. The predictive value of the characteristics of the pain for protozoan infections was calculated.

Results:

Of 220 included patients (92 boys, mean age 8.8 years), 215 brought a stool sample; 73 (34%) carried parasites, 10 of whom had 2 parasites, 2 had 3 parasites. Sixty‐five patients were treated. Twenty‐five (11%) were pain‐free after eradication (21 had D fragilis, 8 B hominis, 4 G lamblia), of whom 11 had another infection (2) or constipation (9) as second diagnosis for the pain. Five had recurrence of infection with D fragilis and were again pain‐free with eradication. Patients with protozoa as cause of their pain did not show differences with respect to their presentation when compared with patients with an asymptomatic infection and patients without protozoa.

Conclusions:

Protozoa were found as the cause of pain in 6% to 11% of children with RAP. These patients did not show a characteristic presentation when compared with patients with other causes of abdominal pain.
Differences in Circulating Carnitine Status of Preterm Infants Fed Fortified Human Milk or Preterm Infant Formula
Authors: Bene Judit , Komlósi Katalin , Melegh Bela I. , Decsi Tamás , Koletzko Berthold , Sauerwald Ulrike
Published: June 2013

Objective:

The aim of the study was to compare plasma carnitine profiles in fortified human milk (HM)–fed preterm infants or formula‐fed preterm infants.

Methods:

Plasma acylcarnitine concentrations were determined in 20 formula‐fed and 18 HM‐fed preterm infants (birth weights between 1000 and 2200 g) by isotope dilution ESI MS/MS technique on study days 0, 14, and 28.

Results:

Concentrations of free carnitine (FC) and different acylcarnitines did not change during the 4 weeks of the study in infants fed HM. In contrast, in infants fed formula FC increased markedly (day 0: 29.989 [16.646] μmol/L, median [interquartile range], day 14: 43.972 [8.455], P < 0.05) along with increases of short‐chain esters (C2 day 0: 5.300 [3.272], day 14: 6.773 [2.127], P < 0.05; C3 day 0: 0.070 [0.059], day 14: 0.110 [0.069], P < 0.05). In contrast, some medium‐chain (C8:1, C12) and long‐chain esters (C14, C16) decreased significantly in infant formula by day 14, whereas FC and C2 and C3 esters increased further by day 28 (FC: 47.672 [14.753], C2: 7.430 [4.688], C3: 0.107 [0.047]).

Conclusions:

The altered carnitine ester profile likely reflects active involvement of the carnitine molecule in the buffering, metabolism, and elimination of nonphysiological acyl moieties.
A natural O-ring optimizes the dispersal of fungal spores
Authors: Fritz Joerg A. , Seminara Agnese , Roper Marcus , Pringle Anne , Brenner Michael P.
Published: June 2013

The forcibly ejected spores of ascomycete fungi must penetrate several millimetres of nearly still air surrounding sporocarps to reach dispersive airflows, and escape is facilitated when a spore is launched with large velocity. To launch, the spores of thousands of species are ejected through an apical ring, a small elastic pore. The startling diversity of apical ring and spore shapes and dimensions make them favoured characters for both species descriptions and the subsequent inference of relationships among species. However, the physical constraints shaping this diversity and the adaptive benefits of specific morphologies are not understood. Here, we develop an elastohydrodynamic theory of the spore's ejection through the apical ring and demonstrate that to avoid enormous energy losses during spore ejection, the four principal morphological dimensions of spore and apical ring must cluster within a nonlinear one-dimensional subspace. We test this prediction using morphological data for 45 fungal species from two different classes and 18 families. Our sampling encompasses multiple loss and gain events and potentially independent origins of this spore ejection mechanism. Although the individual dimensions of the spore and apical ring are only weakly correlated with each other, they collapse into the predicted subspace with high accuracy. The launch velocity appears to be within 2 per cent of the optimum for over 90 per cent of all forcibly ejected species. Although the morphological diversity of apical rings and spores appears startlingly diverse, a simple principle can be used to organize it.
Exploration–exploitation trade-off features a saltatory search behaviour
Authors: Volchenkov Dimitri , Helbach Jonathan , Tscherepanow Marko , Kühnel Sina
Published: June 2013

Searching experiments conducted in different virtual environments over a gender-balanced group of people revealed a gender irrelevant scale-free spread of searching activity on large spatio-temporal scales. We have suggested and solved analytically a simple statistical model of the coherent-noise type describing the exploration–exploitation trade-off in humans (‘should I stay’ or ‘should I go’). The model exhibits a variety of saltatory behaviours, ranging from Lévy flights occurring under uncertainty to Brownian walks performed by a treasure hunter confident of the eventual success.
Collective behaviour of large number of vortices in the plane
Authors: Chen Yuxin , Kolokolnikov Theodore , Zhirov Daniel
Published: June 2013

We investigate the dynamics of
N
point vortices in the plane, in the limit of large
N
. We consider
relative equilibria
, which are rigidly rotating lattice-like configurations of vortices. These configurations were observed in several recent experiments. We show that these solutions and their stability are fully characterized via a related
aggregation model
which was recently investigated in the context of biological swarms. By using this connection, we give explicit analytical formulae for many of the configurations that have been observed experimentally. These include configurations of vortices of equal strength; the
N
+1 configurations of
N
vortices of equal strength and one vortex of much higher strength; and more generally,
N
+
K
configurations. We also give examples of configurations that have not been studied experimentally, including
N
+2 configurations, where
N
vortices aggregate inside an ellipse. Finally, we introduce an artificial ‘damping’ to the vortex dynamics, in an attempt to explain the phenomenon of crystallization that is often observed in real experiments. The diffusion breaks the conservative structure of vortex dynamics, so that any initial conditions converge to the lattice-like relative equilibrium.
Assessing pneumococcal meningitis association with viral respiratory infections and antibiotics: insights from statistical and mathematical models
Authors: Opatowski Lulla , Varon Emmanuelle , Dupont Claire , Temime Laura , van der Werf Sylvie , Gutmann Laurent , Boëlle Pierre-Yves , Watier Laurence , Guillemot Didier
Published: June 2013

Pneumococcus is an important human pathogen, highly antibiotic resistant and a major cause of bacterial meningitis worldwide. Better prevention requires understanding the drivers of pneumococcal infection incidence and antibiotic susceptibility. Although respiratory viruses (including influenza) have been suggested to influence pneumococcal infections, the underlying mechanisms are still unknown, and viruses are rarely considered when studying pneumococcus epidemiology. Here, we propose a novel mathematical model to examine hypothetical relationships between
Streptococcus pneumoniae
meningitis incidence (SPMI), acute viral respiratory infections (AVRIs) and antibiotic exposure. French time series of SPMI, AVRI and penicillin consumption over 2001–2004 are analysed and used to assess four distinct virus–bacteria interaction submodels, ascribing the interaction on pneumococcus transmissibility and/or pathogenicity. The statistical analysis reveals strong associations between time series: SPMI increases shortly after AVRI incidence and decreases overall as the antibiotic-prescription rate rises. Model simulations require a combined impact of AVRI on both pneumococcal transmissibility (up to 1.3-fold increase at the population level) and pathogenicity (up to threefold increase) to reproduce the data accurately, along with diminished epidemic fitness of resistant pneumococcal strains causing meningitis (0.97 (0.96–0.97)). Overall, our findings suggest that AVRI and antibiotics strongly influence SPMI trends. Consequently, vaccination protecting against respiratory virus could have unexpected benefits to limit invasive pneumococcal infections.
Too risky to settle: avian community structure changes in response to perceived predation risk on adults and offspring
Authors: Hua Fangyuan , Fletcher Robert J. , Sieving Kathryn E. , Dorazio Robert M.
Published: June 2013

Predation risk is widely hypothesized as an important force structuring communities, but this potential force is rarely tested experimentally, particularly in terrestrial vertebrate communities. How animals respond to predation risk is generally considered predictable from species life-history and natural-history traits, but rigorous tests of these predictions remain scarce. We report on a large-scale playback experiment with a forest bird community that addresses two questions: (i) does perceived predation risk shape the richness and composition of a breeding bird community? And (ii) can species life-history and natural-history traits predict prey community responses to different types of predation risk? On 9 ha plots, we manipulated cues of three avian predators that preferentially prey on either adult birds or offspring, or both, throughout the breeding season. We found that increased perception of predation risk led to generally negative responses in the abundance, occurrence and/or detection probability of most prey species, which in turn reduced the species richness and shifted the composition of the breeding bird community. Species-level responses were largely predicted from the key natural-history trait of body size, but we did not find support for the life-history theory prediction of the relationship between species' slow/fast life-history strategy and their response to predation risk.
Variation in breeding phenology provides insights into drivers of long-term population change in harbour seals
Authors: Cordes Line S. , Thompson Paul M.
Published: June 2013

Phenological trends provide important indicators of environmental change and population dynamics. However, the use of untested population-level measures can lead to incorrect conclusions about phenological trends, particularly when changes in population structure or density are ignored. We used individual-based estimates of birth date and lactation duration of harbour seals (Phoca vitulina) to investigate energetic consequences of changes in pupping phenology. Using generalized linear mixed models, we first demonstrate annual variation in pupping phenology. Second, we show a negative relationship between lactation duration and the timing of pupping, indicating that females who pup early nurse their pups longer, thereby highlighting lactation duration as a useful proxy of female condition and resource availability. Third, individual-based data were used to derive a population-level proxy that demonstrated an advance in pupping date over the last 25 years, co-incident with a reduction in population abundance that resulted from fisheries-related shootings. These findings demonstrate that phenological studies examining the impacts of climate change on mammal populations must carefully control for changes in population density and highlight how joint investigations of phenological and demographic change provide insights into the drivers of population declines.
Sex-linked transcriptional divergence in the hermaphrodite fungusNeurospora tetrasperma
Authors: Samils Nicklas , Gioti Anastasia , Karlsson Magnus , Sun Yu , Kasuga Takao , Bastiaans Eric , Wang Zheng , Li Ning , Townsend Jeffrey P. , Johannesson Hanna
Published: June 2013

In the filamentous ascomyceteNeurospora tetrasperma, a large (approx. 7 Mbp) region of suppressed recombination surrounds the mating-type (mat) locus. While the remainder of the genome is largely homoallelic, this region of recombinational suppression, extending over 1500 genes, is associated with sequence divergence. Here, we used microarrays to examine how the molecular phenotype of gene expression level is linked to this divergent region, and thus to the mating type. CulturingN. tetraspermaon agar media that induce sexual/female or vegetative/male tissue, we found 196 genes significantly differentially expressed betweenmat Aandmat amating types. Our data show that the genes exhibitingmat-linked expression are enriched in the region genetically linked to mating type, and sequence and expression divergence are positively correlated. Our results indicate that the phenotype ofmat Astrains is optimized for traits promoting sexual/female development and the phenotype ofmat astrains for vegetative/male development. This discovery of differentially expressed genes associated with mating type provides a link between genotypic and phenotypic divergence in this taxon and illustrates a fungal analogue to sexual dimorphism found among animals and plants.
Parental provisioning behaviour plays a key role in linking personality with reproductive success
Authors: Mutzel A. , Dingemanse N. J. , Araya-Ajoy Y. G. , Kempenaers B.
Published: June 2013

Repeatable behavioural traits (‘personality’) have been shown to covary with fitness, but it remains poorly understood how such behaviour–fitness relationships come about. We applied a multivariate approach to reveal the mechanistic pathways by which variation in exploratory and aggressive behaviour is translated into variation in reproductive success in a natural population of blue tits,Cyanistes caeruleus. Using path analysis, we demonstrate a key role for provisioning behaviour in mediating the link between personality and reproductive success (number of fledged offspring). Aggressive males fed their nestlings at lower rates than less aggressive individuals. At the same time, their low parental investment was associated with increased female effort, thereby positively affecting fledgling production. Whereas male exploratory behaviour was unrelated to provisioning behaviour and reproductive success, fast-exploring females fed their offspring at higher rates and initiated breeding earlier, thus increasing reproductive success. Our findings provide strong support for specific mechanistic pathways linking components of behavioural syndromes to reproductive success. Importantly, relationships between behavioural phenotypes and reproductive success were obscured when considering simple bivariate relationships, underlining the importance of adopting multivariate views and statistical tools as path analysis to the study of behavioural evolution.
Eye gaze is not coded by cardinal mechanisms alone
Authors: Cheleski Dominic J. , Mareschal Isabelle , Calder Andrew J. , Clifford Colin W. G.
Published: June 2013

Gaze is an important social cue in regulating human and non-human interactions. In this study, we employed an adaptation paradigm to examine the mechanisms underlying the perception of another's gaze. Previous research has shown that the interleaved presentation of leftwards and rightwards gazing adaptor stimuli results in observers judging a wider range of gaze deviations as being direct. We applied a similar paradigm to examine how human observers encode oblique (e.g. upwards and to the left) directions of gaze. We presented observers with interleaved gaze adaptors and examined whether adaptation differed between congruent (adaptor and test along same axis) and incongruent conditions. We find greater adaptation in congruent conditions along cardinal (horizontal and vertical) and non-cardinal (oblique) directions suggesting gaze is not coded alone by cardinal mechanisms. Our results suggest that the functional aspects of gaze processing might parallel that of basic visual features such as orientation.
The extraembryonic serosa protects the insect egg against desiccation
Authors: Jacobs Chris G. C. , Rezende Gustavo L. , Lamers Gerda E. M. , van der Zee Maurijn
Published: June 2013

Insects have been extraordinarily successful in occupying terrestrial habitats, in contrast to their mostly aquatic sister group, the crustaceans. This success is typically attributed to adult traits such as flight, whereas little attention has been paid to adaptation of the egg. An evolutionary novelty of insect eggs is the serosa, an extraembryonic membrane that enfolds the embryo and secretes a cuticle. To experimentally test the protective function of the serosa, we exploit an exceptional possibility to eliminate this membrane byzerknüllt1RNAi in the beetleTribolium castaneum. We analyse hatching rates of eggs under a range of humidities and find dramatically decreasing hatching rates with decreasing humidities for serosa-less eggs, but not for control eggs. Furthermore, we show serosal expression ofTc-chitin-synthase1and demonstrate that its knock-down leads to absence of the serosal cuticle and a reduction in hatching rates at low humidities. These developmental genetic techniques in combination with ecological testing provide experimental evidence for a crucial role of the serosa in desiccation resistance. We propose that the origin of this extraembryonic membrane facilitated the spectacular radiation of insects on land, as did the origin of the amniote egg in the terrestrial invasion of vertebrates.
The Arabidopsis SWR1 Chromatin-Remodeling Complex Is Important for DNA Repair, Somatic Recombination, and Meiosis
Authors: Rosa Marisa , Von Harder Mona , Aiese Cigliano Riccardo , Schlögelhofer Peter , Mittelsten Scheid Ortrun
Published: June 2013

All processes requiring interaction with DNA are attuned to occur within the context of the complex chromatin structure. As it does for programmed transcription and replication, this also holds true for unscheduled events, such as repair of DNA damage. Lesions such as double-strand breaks occur randomly; their repair requires that enzyme complexes access DNA at potentially any genomic site. This is achieved by chromatin remodeling factors that can locally slide, evict, or change nucleosomes. Here, we show that the Swi2/Snf2-related (SWR1 complex), known to deposit histone H2A.Z, is also important for DNA repair in Arabidopsis thaliana. Mutations in genes for Arabidopsis SWR1 complex subunits PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1, ACTIN-RELATED PROTEIN6, and SWR1 COMPLEX6 cause hypersensitivity to various DNA damaging agents. Even without additional genotoxic stress, these mutants show symptoms of DNA damage accumulation. The reduced DNA repair capacity is connected with impaired somatic homologous recombination, in contrast with the hyper-recombinogenic phenotype of yeast SWR1 mutants. This suggests functional diversification between lower and higher eukaryotes. Finally, reduced fertility and irregular gametogenesis in the Arabidopsis SWR1 mutants indicate an additional role for the chromatin-remodeling complex during meiosis. These results provide evidence for the importance of Arabidopsis SWR1 in somatic DNA repair and during meiosis.
Two hydrate pseudopolymorphs of thiamine pyrophosphate: a dihydrate and a trihydrate
Authors: Li Shu-Qiang , Hu Ning-Hai
Published: June 2013

Two hydrate pseudopolymorphs of 3-[(4-amino-2-methylpyrimidin-1-ium-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl hydrogen pyrophosphate (TPP),viz.a dihydrate, C12H18N4O7P2S·2H2O, (I), and a trihydrate, C12H18N4O7P2S·3H2O, (II), were obtained during a structural study of vitamin B1 coenzyme. In both compounds, TPP is a neutral zwitterion, with its pyrophosphate group doubly deprotonated and its pyrimidine ring protonated, and it assumes the usual `F' conformation in terms of the two torsion angles about the bonds by which the methylene group links the thiazolium and pyrimidinium rings [1.1 (3) and 79.7 (3)° for (I), and 2.0 (3) and 75.5 (3)° for (II)]. In (I), two TPP molecules are linked by a pair of O—H...O hydrogen bonds into a phosphate-pairing dimer. N—H...O hydrogen bonds connect the dimers into a sheet parallel to (101). In (II), the TPP molecules are self-assembled solely by N—H...O hydrogen bonds, generating a tape structure along [001]. A comparison of the four known hydrate pseudopolymorphs of TPP shows that the phosphate-pairing dimers are basic building units for the formation of two-dimensional networks.
Does the likelihood of an Allee effect on plant fecundity depend on the type of pollinator?
Authors: Duffy Karl J. , Patrick Kirsten L. , Johnson Steven D.
Published: June 2013

Factors underlying the Allee effect are still heavily debated in ecology. For plants that rely on pollinators for seed production, decreases in conspecific aggregation may reduce attractiveness to floral visitors and lead to an Allee effect. However, floral visitors often differ in their pollination effectiveness; hence, the likelihood of an Allee effect in plant fecundity may depend on how various flower visitors respond to plant aggregation.

We tested for Allee effects on fecundity of individuals across two years in the self‐incompatible perennial, Kniphofia linearifolia Baker (Xanthorrhoeaceae), which has two distinct types of pollinator, birds and native bees.

For this, we used three measures of aggregation; population size, density and isolation. We made replicated pollinator observations in populations of various aggregations and quantified fecundity in these populations. To determine the differences in pollinator effectiveness and assess their contribution to fecundity, we selectively excluded bird visitors from K. linearifolia in these populations.

We found that population size, but not density or isolation distance, was associated with increased bird abundance and seed set in one of the two years of the study. Bird visitation rate increased with increased plant aggregation within populations. Fruit set and seed set per flower were positively related to bird visitation rate. The difference in seed set per flower between bird‐excluded and unmanipulated plants increased with increasing population size. Although birds were much less frequent visitors than bees (on average 2.1 visits plant−1 h−1 compared to 57.5 visits plant‐1 h−1), selective exclusion experiments indicated that birds are consistently the more effective pollinators of this species, and therefore most likely to influence fecundity.

Synthesis. In this system, characterised by an Allee effect on plant fecundity, birds were the most effective pollinators, responded positively to plant aggregation and were associated with increased fecundity. Therefore, the responses of effective pollinators to plant aggregation may be a factor that underlies Allee effects on plant fecundity.
Occupational therapy and obesity: An integrative literature review
Authors: Haracz Kirsti , Ryan Susan , Hazelton Michael , James Carole
Published: June 2013

Background/aim

Obesity is a significant public health concern globally. It is associated with poor physical health, mental health and subjective well‐being and limitations on occupational participation. With its focus on the relationship between occupation, health and well‐being, occupational therapy would appear to be well placed to address both the causes and consequences of obesity. The aim of this review was to explore the scope of the role of occupational therapy practice in this field and the supporting evidence base.

Methods

Searches were conducted in four online databases and nine occupational therapy journals. Articles were included if they were theoretical, quantitative or qualitative research, explicitly related to occupational therapy and obesity, published in peer‐reviewed journals, in English between 2002 and 2012. All research articles were critically reviewed and thematic analysis was conducted across all of the articles in the review.

Results

Eight theoretical articles, 12 quantitative and two qualitative research studies were included. Only three were outcome studies. Thematic analysis identified four categories of focus of occupational therapy intervention: health promotion and prevention, increasing physical activity participation, modifying dietary intake and reducing the impact of obesity. Four categories of intervention strategies were also identified; assessment, modifying the environment, education and introducing and adapting occupations.

Conclusion and significance

The findings of this review suggest a comprehensive role for occupational therapy in addressing obesity. However, the paucity of outcome studies mean that significantly more research is required to further define and provide a strong evidence base for occupational therapy practice in this emerging field.
Acute intermittent hypoxia induced neural plasticity in respiratory motor control
Authors: Xing Tao , Fong Angelina Y , Bautista Tara G , Pilowsky Paul M
Published: June 2013

Respiratory neural networks can adapt to rapid environmental change or be altered over the long term by various inputs. The mechanisms that underlie the plasticity necessary for adaptive changes in breathing remain unclear. Acute intermittent hypoxia (AIH)‐induced respiratory long‐term facilitation (LTF) is one of the most extensively studied types of respiratory plasticity.

Acute intermittent hypoxia‐induced LTF is present in several respiratory motor outputs, innervating both pump muscles (i.e. diaphragm) and valve muscles (i.e. tongue, pharynx and larynx). Long‐term facilitation is present in various species, including humans, and the expression of LTF is influenced by gender, age and genetics.

Serotonin plays a key role in initiating and modulating plasticity at the level of respiratory motor neurons. Recently, multiple intracellular pathways have been elucidated that are capable of giving rise to respiratory LTF. These mainly activate the metabolic receptors coupled to Gq (‘Q’ pathway) and Gs (‘S’ pathway) proteins.

Herein, we discuss AIH‐induced respiratory LTF in animals and humans, as well as recent advances in our understanding of the synaptic and intracellular pathways underlying this form of plasticity. We also discuss the potential to use intermittent hypoxia to induce functional recovery following cervical spinal injury.
Macroecology of methane‐oxidizing bacteria: the β‐diversity of pmoA genotypes in tropical and subtropical rice paddies
Authors: Lüke Claudia , Frenzel Peter , Ho Adrian , Fiantis Dian , Schad Peter , Schneider Bellinda , Schwark Lorenz , Utami Sri Rahayu
Published: June 2013

Studies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance–decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of β‐diversity with geographical distance across continents (12 000 km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in‐depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three‐dimensional space (multidimensional scaling). The ordination suggests that type II methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II methanotrophs.
Targeting spatiotemporal dynamics of planktonic SAGMGC‐1 and segregation of ammonia‐oxidizing thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction
Authors: Restrepo‐Ortiz Claudia X. , Auguet Jean‐Christophe , Casamayor Emilio O.
Published: June 2013

The annual dynamics of three different ammonia‐oxidizing archaea (AOA) ecotypes (amoA gene) and of the SAGMGC‐1 (Nitrosotalea‐like aquatic Thaumarchaeota) group (16S rRNA gene) were studied by newly designed specific primers and quantitative polymerase chain reaction analysis in a deep oligotrophic high mountain lake (Lake Redon, Limnological Observatory of the Pyrenees, Spain). We observed segregated distributions of the main AOA populations, peaking separately in time and space, and under different ammonia concentrations and irradiance conditions. Strong positive correlation in gene abundances was found along the annual survey between 16S rRNA SAGMAGC‐1 and one of the amoA ecotypes suggesting the potential for ammonia oxidation in the freshwater SAGMAGC‐1 clade. We also observed dominance of Nitrosotalea‐like ecotypes over Nitrosopumilus‐like (Marine Group 1.1a) and not the same annual dynamics for the two thaumarchaeotal clades. The fine scale segregation in space and time of the different AOA ecotypes indicated the presence of phylogenetically close but ecologically segregated AOA species specifically adapted to specific environmental conditions. It remains to be elucidated what would be such environmental drivers.
Mild gut inflammation modulates the proteome of intestinal Escherichia coli
Authors: Schumann Sara , Alpert Carl , Engst Wolfram , Klopfleisch Robert , Loh Gunnar , Bleich André , Blaut Michael
Published: June 2013

Using interleukin 10‐deficient (IL‐10‐/‐) and wild‐type mice monoassociated with either the adherent‐invasive Escherichia coli UNC or the probiotic E. coli Nissle, the effect of a mild intestinal inflammation on the bacterial proteome was studied. Within 8 weeks, IL‐10‐/‐ mice monoassociated with E. coli UNC exhibited an increased expression of several proinflammatory markers in caecal mucosa. Escherichia coli Nissle‐associated IL‐10‐/‐ mice did not do so. As observed previously for E. coli from mice with acute colitis, glycolytic enzymes were downregulated in intestinal E. coli UNC from IL‐10‐/‐ mice. In addition, the inhibitor of vertebrate C‐type lysozyme, Ivy, was upregulated on messenger RNA (mRNA) and protein level in E. coli Nissle from IL‐10‐/‐ mice compared with E. coli UNC from these mice. Higher expression of Ivy in E. coli Nissle correlated with an improved growth of this probiotic strain in the presence of lysozyme‐ethylenediaminetetraacetic acid (EDTA). By overexpressing Ivy, we demonstrated that Ivy contributes to a higher lysozyme resistance of E. coli, supporting the role of Ivy as a potential fitness factor. However, deletion of Ivy did not alter the growth phenotype of E. coli Nissle in the presence of lysozyme‐EDTA, suggesting the existence of additional lysozyme inhibitors that can take over the function of Ivy.
Randomised controlled trial comparing early home biofeedback physiotherapy with pelvic floor exercises for the treatment of third‐degree tears (EBAPT Trial)
Authors: Peirce C , Murphy C , Fitzpatrick M , Cassidy M , Daly L , O'Connell PR , O'Herlihy C
Published: June 2013

Objective

To compare early home biofeedback physiotherapy with pelvic floor exercises (PFEs) for the initial management of women sustaining a primary third‐degree tear.

Design

Single centre, randomised trial.

Setting

National Maternity Hospital, Dublin, Ireland.

Population

A total of 120 women sustaining a primary third‐degree tear.

Methods

Women were randomised in a one to three ratio: 30 to early postpartum home biofeedback physiotherapy and 90 to PFEs.

Main outcome measures

Differences in anorectal manometry results, Cleveland Clinic continence scores and Rockwood faecal incontinence quality of life scale scores after 3 months of postpartum treatment.

Results

The mean anal resting pressure was 39 ± 13 mmHg in the early biofeedback physiotherapy group and 43 ± 17 mmHg in the PFE group. The mean anal squeeze pressure was 64 ± 17 mmHg in the biofeedback group and 62 ± 23 mmHg in the PFE group. There was no significant difference in anal resting and squeeze pressure values between the groups (P = 0.123 and P = 0.68, respectively). There were no differences in symptom score and quality of life measurements between the groups.

Conclusions

This study demonstrates no added value in using early home biofeedback physiotherapy in the management of women sustaining third‐degree tears. Poor compliance may have contributed because women found it difficult to designate time to using biofeedback.
Responding to Crises: The Problematic Relationship between Security and Justice in The Responsibility to Protect
Authors: Bohm Alexandra
Published: June 2013

The Responsibility to Protect (RtP) report has been hailed by academics and policy makers alike as an important policy development in the international community's potential to protect vulnerable and insecure populations from violence. This article critically assesses the RtP, examining the problems with its particular conception of justice and security based on the nature and source of threats to individuals. It criticises the RtP's focus on crises, arguing that this downplays the importance of systemic, ‘chronic’ problems of injustice and disorder across the globe – and thus the importance of responding to these chronic problems. This emphasis, together with the RtP's focus on civil and political rights over socioeconomic rights, results in the causes of crises being perceived as local, thereby obviating the need to admit the role of the international community in contributing to current crises and systemic injustices. Based on these criticisms, this article concludes that the RtP's narrow conception of the relationship between justice and security will not further the international community's ability to discharge its responsibility towards individuals across the globe.