bluuebunny/crossref_metadata_2025 huggingface dataset:
Advancing a clinically relevant perspective of the clonal nature of cancer
Authors: Ruiz Christian , Lenkiewicz Elizabeth , Evers Lisa , Holley Tara , Robeson Alex , Kiefer Jeffrey , Demeure Michael J. , Hollingsworth Michael A. , Shen Michael , Prunkard Donna , Rabinovitch Peter S. , Zellweger Tobias , Mousses Spyro , Trent Jeffrey M. , Carpten John D. , Bubendorf Lukas , Von Hoff Daniel , Barrett Michael T.
Published: July 2011

Cancers frequently arise as a result of an acquired genomic instability and the subsequent clonal evolution of neoplastic cells with variable patterns of genetic aberrations. Thus, the presence and behaviors of distinct clonal populations in each patient's tumor may underlie multiple clinical phenotypes in cancers. We applied DNA content-based flow sorting to identify and isolate the nuclei of clonal populations from tumor biopsies, which was coupled with array CGH and targeted resequencing. The results produced high-definition genomic profiles of clonal populations from 40 pancreatic adenocarcinomas and a set of prostate adenocarcinomas, including serial biopsies from a patient who progressed to androgen-independent metastatic disease. The genomes of clonal populations were found to have patient-specific aberrations of clinical relevance. Furthermore, we identified genomic aberrations specific to therapeutically responsive and resistant clones arising during the evolution of androgen-independent metastatic prostate adenocarcinoma. We also distinguished divergent clonal populations within single biopsies and mapped aberrations in multiple aneuploid populations arising in primary and metastatic pancreatic adenocarcinoma. We propose that our high-definition analyses of the genomes of distinct clonal populations of cancer cells in patients in vivo can help guide diagnoses and tailor approaches to personalized treatment.
Direct observation of ultrafast-electron-transfer reactions unravels high effectiveness of reductive DNA damage
Authors: Nguyen Jenny , Ma Yuhan , Luo Ting , Bristow Robert G. , Jaffray David A. , Lu Qing-Bin
Published: July 2011

Both water and electron-transfer reactions play important roles in chemistry, physics, biology, and the environment. Oxidative DNA damage is a well-known mechanism, whereas the relative role of reductive DNA damage is unknown. The prehydrated electron (

), a novel species of electrons in water, is a fascinating species due to its fundamental importance in chemistry, biology, and the environment.

is an ideal agent to observe reductive DNA damage. Here, we report both the first in situ femtosecond time-resolved laser spectroscopy measurements of ultrafast-electron-transfer (UET) reactions of

with various scavengers (KNO
3
, isopropanol, and dimethyl sulfoxide) and the first gel electrophoresis measurements of DNA strand breaks induced by

and OH
•
radicals co-produced by two-UV-photon photolysis of water. We strikingly found that
the yield of reductive DNA strand breaks induced by each

is twice the yield of oxidative DNA strand breaks induced by each
OH
•
radical
. Our results not only unravel the long-standing mystery about the relative role of radicals in inducing DNA damage under ionizing radiation, but also challenge the conventional notion that oxidative damage is the main pathway for DNA damage. The results also show the potential of femtomedicine as a new transdisciplinary frontier and the broad significance of UET reactions of

in many processes in chemistry, physics, biology, and the environment.
Enhanced production of low energy electrons by alpha particle impact
Authors: Kim Hong-Keun , Titze Jasmin , Schöffler Markus , Trinter Florian , Waitz Markus , Voigtsberger Jörg , Sann Hendrik , Meckel Moritz , Stuck Christian , Lenz Ute , Odenweller Matthias , Neumann Nadine , Schössler Sven , Ullmann-Pfleger Klaus , Ulrich Birte , Fraga Rui Costa , Petridis Nikos , Metz Daniel , Jung Annika , Grisenti Robert , Czasch Achim , Jagutzki Ottmar , Schmidt Lothar , Jahnke Till , Schmidt-Böcking Horst , Dörner Reinhard
Published: July 2011

Radiation damage to living tissue stems not only from primary ionizing particles but to a substantial fraction from the dissociative attachment of secondary electrons with energies below the ionization threshold. We show that the emission yield of those low energy electrons increases dramatically in ion–atom collisions depending on whether or not the target atoms are isolated or embedded in an environment. Only when the atom that has been ionized and excited by the primary particle impact is in immediate proximity of another atom is a fragmentation route known as interatomic Coulombic decay (ICD) enabled. This leads to the emission of a low energy electron. Over the past decade ICD was explored in several experiments following photoionization. Most recent results show its observation even in water clusters. Here we show the quantitative role of ICD for the production of low energy electrons by ion impact, thus approaching a scenario closer to that of radiation damage by alpha particles: We choose ion energies on the maximum of the Bragg peak where energy is most efficiently deposited in tissue. We compare the electron production after colliding He
+
ions on isolated Ne atoms and on Ne dimers (Ne
2
). In the latter case the Ne atom impacted is surrounded by a most simple environment already opening ICD as a deexcitation channel. As a consequence, we find a dramatically enhanced low energy electron yield. The results suggest that ICD may have a significant influence on cell survival after exposure to ionizing radiation.
Functional prokaryotic–eukaryotic chimera from the pentameric ligand-gated ion channel family
Authors: Duret Guillaume , Van Renterghem Catherine , Weng Yun , Prevost Marie , Moraga-Cid Gustavo , Huon Christèle , Sonner James M. , Corringer Pierre-Jean
Published: July 2011

Pentameric ligand-gated ion channels (pLGICs), which mediate chemo-electric signal transduction in animals, have been recently found in bacteria. Despite clear sequence and 3D structure homology, the phylogenetic distance between prokaryotic and eukaryotic homologs suggests significant structural divergences, especially at the interface between the extracellular (ECD) and the transmembrane (TMD) domains. To challenge this possibility, we constructed a chimera in which the ECD of the bacterial protein GLIC is fused to the TMD of the human α1 glycine receptor (α1GlyR). Electrophysiology in
Xenopus
oocytes shows that it functions as a proton-gated ion channel, thereby locating the proton activation site(s) of GLIC in its ECD. Patch-clamp experiments in BHK cells show that the ion channel displays an anionic selectivity with a unitary conductance identical to that of the α1GlyR. In addition, pharmacological investigations result in transmembrane allosteric modulation similar to the one observed on α1GlyR. Indeed, the clinically active drugs propofol, four volatile general anesthetics, alcohols, and ivermectin all potentiate the chimera while they inhibit GLIC. Collectively, this work shows the compatibility between GLIC and α1GlyR domains and points to conservation of the ion channel and transmembrane allosteric regulatory sites in the chimera. This provides evidence that GLIC and α1GlyR share a highly homologous 3D structure. GLIC is thus a relevant model of eukaryotic pLGICs, at least from the anionic type. In addition, the chimera is a good candidate for mass production in
Escherichia coli
, opening the way for investigations of “druggable” eukaryotic allosteric sites by X-ray crystallography.
Multiscale simulations suggest a mechanism for integrin inside-out activation
Authors: Kalli Antreas C. , Campbell Iain D. , Sansom Mark S. P.
Published: July 2011

Integrins are large cell-surface adhesion receptors that can be activated to a high affinity state by the formation of an intracellular complex between the integrin β-subunit tail, the membrane, and talin. The F2 and F3 subdomains of the talin head play a key role in formation of this complex. Here, activation of the integrin αIIb/β3 dimer by the talin head domain was probed using multiscale molecular dynamics simulations. A number of novel insights emerge from these studies, including (
i
) the importance of the integrin αIIb subunit F992 and F993 residues in stabilizing the “off” state of the αIIb/β3 dimer, (
ii
) a crucial role for negatively charged groups in the F2-F3/membrane interaction, (
iii
) binding of the talin F2-F3 domain to negatively charged lipid headgroups in the membrane induces a reorientation of the β transmembrane (TM) domain, (
iv
) an increase in the tilt angle of the β TM domain relative to the bilayer normal helps to destabilize the α/β TM interaction and promote a scissor-like movement of the integrin TM helices. These results, combined with various published experimental observations, suggest a model for the mechanism of inside-out activation of integrins by talin.
Numerical simulations of the Macondo well blowout reveal strong control of oil flow by reservoir permeability and exsolution of gas
Authors: Oldenburg Curtis M. , Freifeld Barry M. , Pruess Karsten , Pan Lehua , Finsterle Stefan , Moridis George J.
Published: July 2011

In response to the urgent need for estimates of the oil and gas flow rate from the Macondo well MC252-1 blowout, we assembled a small team and carried out oil and gas flow simulations using the TOUGH2 codes over two weeks in mid-2010. The conceptual model included the oil reservoir and the well with a top boundary condition located at the bottom of the blowout preventer. We developed a fluid properties module (Eoil) applicable to a simple two-phase and two-component oil-gas system. The flow of oil and gas was simulated using T2Well, a coupled reservoir-wellbore flow model, along with iTOUGH2 for sensitivity analysis and uncertainty quantification. The most likely oil flow rate estimated from simulations based on the data available in early June 2010 was about 100,000 bbl/d (barrels per day) with a corresponding gas flow rate of 300 MMscf/d (million standard cubic feet per day) assuming the well was open to the reservoir over 30 m of thickness. A Monte Carlo analysis of reservoir and fluid properties provided an uncertainty distribution with a long tail extending down to 60,000 bbl/d of oil (170 MMscf/d of gas). The flow rate was most strongly sensitive to reservoir permeability. Conceptual model uncertainty was also significant, particularly with regard to the length of the well that was open to the reservoir. For fluid-entry interval length of 1.5 m, the oil flow rate was about 56,000 bbl/d. Sensitivity analyses showed that flow rate was not very sensitive to pressure-drop across the blowout preventer due to the interplay between gas exsolution and oil flow rate.
DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation
Authors: Pek Jun Wei , Kai Toshie
Published: July 2011

During mitosis, faithful inheritance of genetic material is achieved by chromosome segregation, as mediated by the condensin I and II complexes. Failed chromosome segregation can result in neoplasm formation, infertility, and birth defects. Recently, the germ-line–specific DEAD-box RNA helicase Vasa was demonstrated to promote mitotic chromosome segregation in
Drosophila
by facilitating robust chromosomal localization of Barren (Barr), a condensin I component. This mitotic function of Vasa is mediated by Aubergine and Spindle-E, which are two germ-line components of the Piwi-interacting RNA pathway. Faithful segregation of chromosomes should be executed both in germ-line and somatic cells. However, whether a similar mechanism also functions in promoting chromosome segregation in somatic cells has not been elucidated. Here, we present evidence that
belle
(
vasa
paralog) and the RNA interference pathway regulate chromosome segregation in
Drosophila
somatic cells. During mitosis,
belle
promotes robust Barr chromosomal localization and chromosome segregation. Belle's localization to condensing chromosomes depends on
dicer-2
and
argonaute2
. Coimmunoprecipitation experiments indicated that Belle interacts with Barr and Argonaute2 and is enriched at endogenous siRNA (endo-siRNA)-generating loci. Our results suggest that Belle functions in promoting chromosome segregation in
Drosophila
somatic cells via the endo-siRNA pathway.
DDX3
(human homolog of
belle
) and
DICER
function in promoting chromosome segregation and hCAP-H (human homolog of Barr) localization in HeLa cells, indicating a conserved function for those proteins in human cells. Our results suggest that the RNA helicase Belle/DDX3 and the RNA interference pathway perform a common role in regulating chromosome segregation in
Drosophila
and human somatic cells.
Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases
Authors: Hauschild Janet , Petersen Bjoern , Santiago Yolanda , Queisser Anna-Lisa , Carnwath Joseph W. , Lucas-Hahn Andrea , Zhang Lei , Meng Xiangdong , Gregory Philip D. , Schwinzer Reinhard , Cost Gregory J. , Niemann Heiner
Published: July 2011

Zinc-finger nucleases (ZFNs) are powerful tools for producing gene knockouts (KOs) with high efficiency. Whereas ZFN-mediated gene disruption has been demonstrated in laboratory animals such as mice, rats, and fruit flies, ZFNs have not been used to disrupt an endogenous gene in any large domestic species. Here we used ZFNs to induce a biallelic knockout of the porcine α1,3-galactosyltransferase (GGTA1) gene. Primary porcine fibroblasts were treated with ZFNs designed against the region coding for the catalytic core ofGGTA1, resulting in biallelic knockout of ∼1% of ZFN-treated cells. A galactose (Gal) epitope counter-selected population of these cells was used in somatic cell nuclear transfer (SCNT). Of the resulting six fetuses, all completely lacked Gal epitopes and were phenotypically indistinguishable from the starting donor cell population, illustrating that ZFN-mediated genetic modification did not interfere with the cloning process. Neither off-target cleavage events nor integration of the ZFN-coding plasmid was detected. TheGGTA1-KO phenotype was confirmed by a complement lysis assay that demonstrated protection ofGGTA1-KO fibroblasts relative to wild-type cells. Cells fromGGTA1-KO fetuses and pooled, transfected cells were used to produce live offspring via SCNT. This study reports the production of cloned pigs carrying a biallelic ZFN-induced knockout of an endogenous gene. These findings open a unique avenue toward the creation of gene KO pigs, which could benefit both agriculture and biomedicine.
Simplifying the representation of complex free-energy landscapes using sketch-map
Authors: Ceriotti Michele , Tribello Gareth A. , Parrinello Michele
Published: July 2011

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.
Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data
Authors: Tao Yong , Ruan Jue , Yeh Shiou-Hwei , Lu Xuemei , Wang Yu , Zhai Weiwei , Cai Jun , Ling Shaoping , Gong Qiang , Chong Zecheng , Qu Zhengzhong , Li Qianqian , Liu Jiang , Yang Jin , Zheng Caihong , Zeng Changqing , Wang Hurng-Yi , Zhang Jing , Wang Sheng-Han , Hao Lingtong , Dong Lili , Li Wenjie , Sun Min , Zou Wei , Yu Caixia , Li Chaohua , Liu Guojing , Jiang Lan , Xu Jin , Huang Huanwei , Li Chunyan , Mi Shuangli , Zhang Bing , Chen Baoxian , Zhao Wenming , Hu Songnian , Zhuang Shi-Mei , Shen Yang , Shi Suhua , Brown Christopher , White Kevin P. , Chen Ding-Shinn , Chen Pei-Jer , Wu Chung-I
Published: July 2011

We present the analysis of the evolution of tumors in a case of hepatocellular carcinoma. This case is particularly informative about cancer growth dynamics and the underlying driving mutations. We sampled nine different sections from three tumors and seven more sections from the adjacent nontumor tissues. Selected sections were subjected to exon as well as whole-genome sequencing. Putative somatic mutations were then individually validated across all 9 tumor and 7 nontumor sections. Among the mutations validated, 24 were amino acid changes; in addition, 22 large indels/copy number variants (>1 Mb) were detected. These somatic mutations define four evolutionary lineages among tumor cells. Separate evolution and expansion of these lineages were recent and rapid, each apparently having only one lineage-specific protein-coding mutation. Hence, by using a cell-population genetic definition, this approach identified three coding changes (CCNG1, P62, and an indel/fusion gene) as tumor driver mutations. These three mutations, affecting cell cycle control and apoptosis, are functionally distinct from mutations that accumulated earlier, many of which are involved in inflammation/immunity or cell anchoring. These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth.
Rerooting the evolutionary tree of malaria parasites
Authors: Outlaw Diana C. , Ricklefs Robert E.
Published: July 2011

Malaria parasites (
Plasmodium
spp.) have plagued humans for millennia. Less well known are related parasites (Haemosporida), with diverse life cycles and dipteran vectors that infect other vertebrates. Understanding the evolution of parasite life histories, including switches between hosts and vectors, depends on knowledge of evolutionary relationships among parasite lineages. In particular, inferences concerning time of origin and trait evolution require correct placement of the root of the evolutionary tree. Phylogenetic reconstructions of the diversification of malaria parasites from DNA sequences have suffered from uncertainty concerning outgroup taxa, limited taxon sampling, and selection on genes used to assess relationships. As a result, inferred relationships among the Haemosporida have been unstable, and questions concerning evolutionary diversification and host switching remain unanswered. A recent phylogeny placed mammalian malaria parasites, as well as avian/reptilian
Plasmodium
, in a derived position relative to the avian parasite genera
Leucocytozoon
and
Haemoproteus
, implying that the ancestral forms lacked merogony in the blood and that their vectors were non-mosquito dipterans. Bayesian, outgroup-free phylogenetic reconstruction using relaxed molecular clocks with uncorrelated rates instead suggested that mammalian and avian/reptilian
Plasmodium
parasites, spread by mosquito vectors, are ancestral sister taxa, from which a variety of specialized parasite lineages with modified life histories have evolved.
Structural and functional analysis of PTPMT1, a phosphatase required for cardiolipin synthesis
Authors: Xiao Junyu , Engel James L. , Zhang Ji , Chen Mark J. , Manning Gerard , Dixon Jack E.
Published: July 2011

PTPMT1 (PTP localized to the Mitochondrion 1) is a member of the protein tyrosine phosphatase superfamily that is localized exclusively to the mitochondrion. We recently reported that PTPMT1 dephosphorylates phosphatidylglycerol phosphate, an essential intermediate of cardiolipin biosynthesis. To gain further insights into the molecular basis of PTPMT1 function, we determined the crystal structures of the phosphatase domain of PTPMT1. PTPMT1 exhibits a canonical protein tyrosine phosphatase domain fold, resembling many dual-specificity phosphatases such as phosphatase and tensin homolog and vaccinia H1-related phosphatase. We also determined the structure of the catalytically inactive phosphatase in complex with a surrogate substrate, phosphatidylinositol 5-phosphate, which sheds light on the substrate recognition and specificity of PTPMT1. Comparison of the apo and substrate-bound structures of PTPMT1 suggests that it undergoes significant conformational change during catalysis, and we further demonstrated that an evolutionarily conserved EEYE loop is important for its activity.
African monkeys are infected by
Plasmodium falciparum
nonhuman primate-specific strains
Authors: Prugnolle Franck , Ollomo Benjamin , Durand Patrick , Yalcindag Erhan , Arnathau Céline , Elguero Eric , Berry Antoine , Pourrut Xavier , Gonzalez Jean-Paul , Nkoghe Dieudonné , Akiana Jean , Verrier Delphine , Leroy Eric , Ayala Francisco J. , Renaud François
Published: July 2011

Recent molecular exploration of the
Plasmodium
species circulating in great apes in Africa has revealed the existence of a large and previously unknown diversity of
Plasmodium
. For instance, gorillas were found to be infected by parasites closely related to
Plasmodium falciparum
, suggesting that the human malignant malaria agent may have arisen after a transfer from gorillas. Although this scenario is likely in light of the data collected in great apes, it remained to be ascertained whether
P. falciparum
-related parasites may infect other nonhuman primates in Africa. Using molecular tools, we here explore the diversity of
Plasmodium
species infecting monkeys in Central Africa. In addition to previously described
Hepatocystis
and
Plasmodium
species (
Plasmodium gonderi and Plasmodium sp DAJ-2004
), we have found one African monkey to be infected by a
P. falciparum
-related parasite. Examination of the nuclear and mitochondrial genomes of this parasite reveals that it is specific of nonhuman primates, indicating that
P. falciparum
-related pathogens can naturally circulate in some monkey populations in Africa. We also show that at least two distinct genetic entities of
P. falciparum
infect nonhuman primates and humans, respectively. Our discoveries bring into question the proposed gorilla origin of human
P. falciparum
.
DNA methylation regulates phenotype-dependent transcriptional activity in
Candida albicans
Authors: Mishra Prashant K. , Baum Mary , Carbon John
Published: July 2011

DNA methylation is a common epigenetic signaling mechanism associated with silencing of repeated DNA and transcriptional regulation in eukaryotes. Here we report that DNA methylation in the human fungal pathogen
Candida albicans
is primarily localized within structural genes and modulates transcriptional activity. Major repeat sequences and multigene families are largely free of DNA methylation. Among the genes subject to DNA methylation are those associated with dimorphic transition between yeast and hyphal forms, switching between white and opaque cells, and iron metabolism. Transcriptionally repressed methylated loci showed increased frequency of C-to-T transitions during asexual growth, an evolutionarily stable pattern of repression associated mutation that could bring about genetic alterations under changing environmental or host conditions. Dynamic differential DNA methylation of structural genes may be one factor contributing to morphological plasticity that is cued by nutrition and host interaction.
Complex permeability and microwave absorption properties of Y2Fe17 micropowders with planar anisotropy
Authors: Chi Xiao , Yi Haibo , Zuo Wenliang , Qiao Liang , Wang Tao , Li Fashen
Published: July 2011

Planar anisotropy Y2Fe17 powders were fabricated by rapid quenching and ball-milling techniques. The frequency dependence of complex permeability and permittivity of paraffin composites with 35 vol% Y2Fe17 powders have been investigated in the frequency range 0.1–10 GHz. The oriented composite shows a dramatic increase in permeability and a remarkable decrease in the matching thickness. The minimum reflection losses of unoriented Y2Fe17 composite and oriented Y2Fe17 composite were −48 dB at 2.34 GHz and −59 dB at 3.4 GHz, and the corresponding thicknesses were only 3.9 mm and 2.3 mm, respectively. Otherwise, the product of the static permeability and the resonance frequency for the oriented Y2Fe17 compound is 91.6 GHz, which is much higher than the value of 15.3 GHz calculated by Snoek's limit equation. Hence, the Y2Fe17 composite, with the specific property of the planar anisotropy, has great potential applications in the field of high-frequency microwave absorption.
A novel approach to the synthesis of CoPt magnetic nanoparticles
Authors: Zhang Y J , Yang Y T , Liu Y , Wang Y X , Yang L L , Wei M B , Fan H G , Zhai H J , Liu X Y , Liu Y Q , Yang N N , Wu Y H , Yang J H
Published: July 2011

L10 CoPt nanoparticles with face-centred tetragonal (FCT) structure are synthesized by the sol–gel method. Differential thermal analyses show the dehydration of various water molecules and decomposition/combustion of organic groups at a temperature below 600 °C and melting of Co and Pt at 700 °C. X-ray diffraction results show a transition from face-centred cubic to the FCT phase and an increase in particle size with increasing temperature. Transmission electron microscope (TEM) images show that highly monodisperse particles are obtained. High-resolution TEM (HRTEM) images reveal the appearance of L10 ordered phase at temperatures above 600 °C. The survey scans of x-ray photoelectron spectroscopy show that no magnetic impurity is detected within the detection limit. The maximum coercivity (353 344 A m−1) is obtained for the samples heated at 800 °C. The relationship between the temperature and the structure is discussed and the possible growth mechanism is given in terms of atomic diffusion.
Analysis of the oscillating photocarrier grating technique
Authors: Ventosinos F , Budini N , Longeaud C , Schmidt J A
Published: July 2011

In this paper we present a complete theoretical analysis of the oscillating photocarrier grating (OPG) method, starting from the generalized equations that describe charge transport and recombination under oscillating grating illumination conditions. The solution of these equations allows us to implement a calculation reproducing the experimental OPG curves. We study both experimentally and from our calculations the dependence of the OPG curves on different external parameters, such as the applied electric field, grating period and illumination intensity. We find that the response of the sample is linked to a characteristic time of the material, which could be the dielectric relaxation time or the small signal lifetime depending on the regime at which the experiment is performed. Therefore, the OPG technique provides a simple method to estimate these parameters. In addition, we demonstrate that the small signal lifetime provides information on the density of states of the material.
Source-trap characterization of thermally transferred OSL in quartz
Authors: Shen Z X , Mauz B , Lang A
Published: July 2011

Thermally transferred optically stimulated luminescence (TT-OSL) of quartz is the low intensity OSL measured after heating a previously optically zeroed quartz to temperatures below that erasing the OSL electron trap. We identify the source traps contributing to TT-OSL by studying the changes in TT-OSL and thermoluminescence (TL) caused by optical bleaching at various temperatures and by repeated TT-OSL measurements, and quantify source-trap parameters using the Hoogenstraaten method. We find that both the single transfer mechanism and the double transfer mechanism are contributing to TT-OSL production. Three source traps are identified when the samples are heated to 300 °C for 10 s to induce the thermal transfer. The first one corresponds to a TL peak at ∼200 °C. It captures electrons during the optical bleaching and releases these charges during subsequent heating. It provides ∼10% of the electrons that give rise to TT-OSL. The second trap corresponds to a TL peak at 290–300 °C and provides ∼80% of the electrons for TT-OSL through the single transfer mechanism. This electron trap has a depth of 1.34 ± 0.05 eV and a frequency factor in the order of 1011 s−1. It has a mean lifetime of 0.24 Ma at 10 °C. The third trap corresponds to a TL peak at ∼380 °C and provides ∼10% electrons for TT-OSL through the single transfer mechanism. It has a depth of 1.66 ± 0.07 eV and a frequency factor in the order of 1012 s−1. To validate the techniques used we also determined the parameters of the fast component OSL trap and received results consistent with published values. Most importantly, our results show that the relatively short lifetime of the main TT-OSL source trap limits possibilities of using TT-OSL to extend the age range of quartz OSL dating, as has been suggested by various authors.
Multiple cell configuration electromagnetic vibration energy harvester
Authors: Marin Anthony , Bressers Scott , Priya Shashank
Published: July 2011

This paper reports the design of an electromagnetic vibration energy harvester that doubles the magnitude of output power generated by the prior four-bar magnet configuration. This enhancement was achieved with minor increase in volume by 23% and mass by 30%. The new ‘double cell’ design utilizes an additional pair of magnets to create a secondary air gap, or cell, for a second coil to vibrate within. To further reduce the dimensions of the device, two coils were attached to one common cantilever beam. These unique features lead to improvements of 66% in output power per unit volume (power density) and 27% increase in output power per unit volume and mass (specific power density), from 0.1 to 0.17 mW cm−3 and 0.41 to 0.51 mW cm−3 kg−1 respectively. Using the ANSYS multiphysics analysis, it was determined that for the double cell harvester, adding one additional pair of magnets created a small magnetic gradient between air gaps of 0.001 T which is insignificant in terms of electromagnetic damping. An analytical model was developed to optimize the magnitude of transformation factor and magnetic field gradient within the gap.
Treatment of Acute Diarrhea With Saccharomyces boulardii in Infants
Authors: Corrêa Naflesia B.O. , Penna Francisco J. , Lima Fátima M.L.S. , Nicoli Jacques R. , Filho Luciano A.P.
Published: July 2011

Objective:

The aim of the study was to determine whether an oral treatment with a commercial pharmaceutical product containing Saccharomyces boulardii would reduce the duration of diarrhea in infants with acute diarrhea.

Patients and Methods:

In the present double‐blind, placebo‐controlled study, 186 infants, 6 to 48 months old and hospitalized within 72 hours after the onset of acute diarrhea in 2 hospitals in Goiânia, Goiás, Brazil, were randomly assigned to receive twice per day for 5 days 200 mg of a commercial pharmaceutical product containing 4 × 109 viable cells of S boulardii or a placebo. Stool samples were submitted to search for rotavirus. Among the 176 infants who completed the trial, those treated with S boulardii (90) showed a reduction in diarrhea duration (P < 0.05) when compared with the placebo group (86).

Results:

The present study shows a reduction in diarrhea duration when S boulardii was given to children within 72 hours after the onset of acute diarrhea.

Conclusions:

The present study suggests a complementary treatment of acute diarrhea in infants with daily oral doses of S boulardii.
Long-term cleaner fish presence affects growth of a coral reef fish
Authors: Clague Gillian E. , Cheney Karen L. , Goldizen Anne W. , McCormick Mark I. , Waldie Peter A. , Grutter Alexandra S.
Published: July 2011

Cleaning behaviour is considered to be a classical example of mutualism. However, no studies, to our knowledge, have measured the benefits to clients in terms of growth. In the longest experimental study of its kind, over an 8 year period, cleaner fish
Labroides dimidiatus
were consistently removed from seven patch reefs (61–285 m
2
) and left undisturbed on nine control reefs, and the growth and parasite load of the damselfish
Pomacentrus moluccensis
determined. After 8 years, growth was reduced and parasitic copepod abundance was higher on fish from removal reefs compared with controls, but only in larger individuals. Behavioural observations revealed that
P. moluccensis
cleaned by
L. dimidiatus
were 27 per cent larger than nearby conspecifics. The selective cleaning by
L. dimidiatus
probably explains why only larger
P. moluccensis
individuals benefited from cleaning. This is the first demonstration, to our knowledge, that cleaners affect the growth rate of client individuals; a greater size for a given age should result in increased fecundity at a given time. The effect of the removal of so few small fish on the size of another fish species is unprecedented on coral reefs.
Female choice and extra-pair paternity in a traditional human population
Authors: Scelza Brooke A.
Published: July 2011

Seeking out extra-pair paternity (EPP) is a viable reproductive strategy for females in many pair-bonded species. Across human societies, women commonly engage in extra-marital affairs, suggesting this strategy may also be an important part of women's reproductive decision-making. Here, I show that among the Himba 17 per cent of all recorded marital births are attributed by women to EPP, and EPP is associated with significant increases in women's reproductive success. In contrast, there are no cases of EPP among children born into ‘love match’ marriages. This rate of EPP is higher than has been recorded in any other small-scale society. These results illustrate the importance of seeking EPP as a mechanism of female choice in humans, while simultaneously showing it to be highly variable and context-dependent.
A new navigational mechanism mediated by ant ocelli
Authors: Schwarz Sebastian , Wystrach Antoine , Cheng Ken
Published: July 2011

Many animals rely on path integration for navigation and desert ants are the champions. On leaving the nest, ants continuously integrate their distance and direction of travel so that they always know their current distance and direction from the nest and can take a direct path to home. Distance information originates from a step-counter and directional information is based on a celestial compass. So far, it has been assumed that the directional information obtained from ocelli contribute to a single global path integrator, together with directional information from the dorsal rim area (DRA) of the compound eyes and distance information from the step-counter. Here, we show that ocelli mediate a distinct compass from that mediated by the compound eyes. After travelling a two-leg outbound route, untreated foragers headed towards the nest direction, showing that both legs of the route had been integrated. In contrast, foragers with covered compound eyes but uncovered ocelli steered in the direction opposite to the last leg of the outbound route. Our findings suggest that, unlike the DRA, ocelli cannot by themselves mediate path integration. Instead, ocelli mediate a distinct directional system, which buffers the most recent leg of a journey.
An Early Cambrian stem polychaete with pygidial cirri
Authors: Vinther Jakob , Eibye-Jacobsen Danny , Harper David A. T.
Published: July 2011

The oldest annelid fossils are polychaetes from the Cambrian Period. They are representatives of the annelid stem group and thus vital in any discussion of how we polarize the evolution of the crown group. Here, we describe a fossil polychaete from the Early Cambrian Sirius Passet fauna,
Pygocirrus butyricampum
gen. et sp. nov., with structures identified as pygidial cirri, which are recorded for the first time from Cambrian annelids. The body is slender and has biramous parapodia with chaetae organized in laterally oriented bundles. The presence of pygidial cirri is one of the characters that hitherto has defined the annelid crown group, which diversified during the Cambrian–Ordovician transition. The newly described fossil shows that this character had already developed within the total group by the Early Cambrian.
Biodiversity: past, present and future
Authors: Rubidge Emily M. , Burton A. Cole , Vamosi Steven M.
Published: July 2011

On 12–15 May 2011, a diverse group of students, researchers and practitioners from across Canada and around the world met in Banff, Alberta, to discuss the many facets of biodiversity science at the 6th Annual Meeting of the Canadian Society for Ecology and Evolution.
Role of shear stress and stretch in vascular mechanobiology
Authors: Lu Deshun , Kassab Ghassan S.
Published: July 2011

Blood vessels are under constant mechanical loading from blood pressure and flow which cause internal stresses (endothelial shear stress and circumferential wall stress, respectively). The mechanical forces not only cause morphological changes of endothelium and blood vessel wall, but also trigger biochemical and biological events. There is considerable evidence that physiologic stresses and strains (stretch) exert vasoprotective roles via nitric oxide and provide a homeostatic oxidative balance. A perturbation of tissue stresses and strains can disturb biochemical homeostasis and lead to vascular remodelling and possible dysfunction (e.g. altered vasorelaxation, tone, stiffness, etc.). These distinct biological endpoints are caused by some common biochemical pathways. The focus of this brief review is to point out some possible commonalities in the molecular pathways in response to endothelial shear stress and circumferential wall stretch.
A linear-optical proof that the permanent is #
P
-hard
Authors: Aaronson Scott
Published: July 2011

One of the crown jewels of complexity theory is Valiant's theorem that computing the permanent of an
n
×
n
matrix is

#
P

-hard. Here we show that, by using the model of
linear-optical quantum computing
—and in particular, a universality theorem owing to Knill, Laflamme and Milburn—one can give a different and arguably more intuitive proof of this theorem.
First record of preserved soft parts in a Palaeozoic podocopid (Metacopina) ostracod,
Cytherellina submagna
: phylogenetic implications
Authors: Olempska E. , Horne D. J. , Szaniawski H.
Published: July 2011

The metacopines represent one of the oldest and most important extinct groups of ostracods, with a fossil record from the Mid-Ordovician to the Early Jurassic. Herein, we report the discovery of a representative of the group with three-dimensionally preserved soft parts. The specimen—a male of
Cytherellina submagna
—was found in the Early Devonian (416 Ma) of Podolia, Ukraine. A branchial plate (Bp) of the cephalic maxillula (Mx), a pair of thoracic appendages (walking legs), a presumed furca (Fu) and a copulatory organ are preserved. The material also includes phosphatized steinkerns with exceptionally preserved marginal pore canals and muscle scars. The morphology of the preserved limbs and valves of
C. submagna
suggests its relationship with extant Podocopida, particularly with the superfamilies Darwinuloidea and Sigillioidea, which have many similar characteristic features, including a large Bp on the Mx, the morphology of walking legs, Fu with two terminal claws, internal stop-teeth in the left valve, adductor muscle scar pattern, and a very narrow fused zone along the anterior and posterior margins. More precise determination of affinities will depend on the soft-part morphology of the cephalic segment, which has not been revealed in the present material.
Blood flow to long bones indicates activity metabolism in mammals, reptiles and dinosaurs
Authors: Seymour Roger S. , Smith Sarah L. , White Craig R. , Henderson Donald M. , Schwarz-Wings Daniela
Published: July 2011

The cross-sectional area of a nutrient foramen of a long bone is related to blood flow requirements of the internal bone cells that are essential for dynamic bone remodelling. Foramen area increases with body size in parallel among living mammals and non-varanid reptiles, but is significantly larger in mammals. An index of blood flow rate through the foramina is about 10 times higher in mammals than in reptiles, and even higher if differences in blood pressure are considered. The scaling of foramen size correlates well with maximum whole-body metabolic rate during exercise in mammals and reptiles, but less well with resting metabolic rate. This relates to the role of blood flow associated with bone remodelling during and following activity. Mammals and varanid lizards have much higher aerobic metabolic rates and exercise-induced bone remodelling than non-varanid reptiles. Foramen areas of 10 species of dinosaur from five taxonomic groups are generally larger than from mammals, indicating a routinely highly active and aerobic lifestyle. The simple measurement holds possibilities offers the possibility of assessing other groups of extinct and living vertebrates in relation to body size, behaviour and habitat.
Subordinate male cichlids retain reproductive competence during social suppression
Authors: Kustan Jacqueline M. , Maruska Karen P. , Fernald Russell D.
Published: July 2011

Subordinate males, which are excluded from reproduction often save energy by reducing their investment in sperm production. However, if their position in a dominance hierarchy changes suddenly they should also rapidly attain fertilization capability. Here, we asked how social suppression and ascension to dominance influences sperm quality, spermatogenesis and reproductive competence in the cichlidAstatotilapia burtoni, where reproduction is tightly coupled to social status. Dominant territorial (T) males are reproductively active while subordinate non-territorial (NT) males are suppressed, but given the opportunity, NT males will perform dominance behaviours within minutes and attain T male testes size within days. Using the thymidine analogue 5-bromo-2-deoxyuridine (BrdU) to label germ cell proliferation, we found that the spermatogenic cycle takes approximately 11–12 days, and social status had no effect on proliferation, suggesting that spermatogenesis continues during reproductive suppression. Although sperm velocity did not differ among social states, NT males had reduced sperm motility. Remarkably, males ascending in status showed sperm motility equivalent to T males within 24 h. Males also successfully reproduced within hours of social opportunity, despite four to five weeks of suppression and reduced testis size. Our data suggest that NT males maintain reproductive potential during suppression possibly as a strategy to rapidly improve reproductive fitness upon social opportunity.
Bad to the bone: facial structure predicts unethical behaviour
Authors: Haselhuhn Michael P. , Wong Elaine M.
Published: July 2011

Researchers spanning many scientific domains, including primatology, evolutionary biology and psychology, have sought to establish an evolutionary basis for morality. While researchers have identified social and cognitive adaptations that support ethical behaviour, a consensus has emerged that genetically determinedphysicaltraits are not reliable signals of unethical intentions or actions. Challenging this view, we show that genetically determined physical traits can serve as reliable predictors of unethical behaviour if they are also associated with positive signals in intersex and intrasex selection. Specifically, we identify a key physical attribute, the facial width-to-height ratio, which predicts unethical behaviour in men. Across two studies, we demonstrate that men with wider faces (relative to facial height) are more likely to explicitly deceive their counterparts in a negotiation, and are more willing to cheat in order to increase their financial gain. Importantly, we provide evidence that the link between facial metrics and unethical behaviour is mediated by a psychological sense of power. Our results demonstrate that static physical attributes can indeed serve as reliable cues of immoral action, and provide additional support for the view that evolutionary forces shape ethical judgement and behaviour.
Benzoxazinoid Metabolites Regulate Innate Immunity against Aphids and Fungi in Maize
Authors: Ahmad Shakoor , Veyrat Nathalie , Gordon-Weeks Ruth , Zhang Yuhua , Martin Janet , Smart Lesley , Glauser Gaétan , Erb Matthias , Flors Victor , Frey Monika , Ton Jurriaan
Published: July 2011

Benzoxazinoids (BXs), such as 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), are secondary metabolites in grasses. The first step in BX biosynthesis converts indole-3-glycerol phosphate into indole. In maize (Zea mays), this reaction is catalyzed by either BENZOXAZINELESS1 (BX1) or INDOLE GLYCEROL PHOSPHATE LYASE (IGL). The Bx1 gene is under developmental control and is mainly responsible for BX production, whereas the Igl gene is inducible by stress signals, such as wounding, herbivory, or jasmonates. To determine the role of BXs in defense against aphids and fungi, we compared basal resistance between Bx1 wild-type and bx1 mutant lines in the igl mutant background, thereby preventing BX production from IGL. Compared to Bx1 wild-type plants, BX-deficient bx1 mutant plants allowed better development of the cereal aphid Rhopalosiphum padi, and were affected in penetration resistance against the fungus Setosphaeria turtica. At stages preceding major tissue disruption, R. padi and S. turtica elicited increased accumulation of DIMBOA-glucoside, DIMBOA, and 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one-glucoside (HDMBOA-glc), which was most pronounced in apoplastic leaf extracts. Treatment with the defense elicitor chitosan similarly enhanced apoplastic accumulation of DIMBOA and HDMBOA-glc, but repressed transcription of genes controlling BX biosynthesis downstream of BX1. This repression was also obtained after treatment with the BX precursor indole and DIMBOA, but not with HDMBOA-glc. Furthermore, BX-deficient bx1 mutant lines deposited less chitosan-induced callose than Bx1 wild-type lines, whereas apoplast infiltration with DIMBOA, but not HDMBOA-glc, mimicked chitosan-induced callose. Hence, DIMBOA functions as a defense regulatory signal in maize innate immunity, which acts in addition to its well-characterized activity as a biocidal defense metabolite.
Experimental Evidence of Phosphoenolpyruvate Resynthesis from Pyruvate in Illuminated Leaves
Authors: Tcherkez Guillaume , Mahé Aline , Boex-Fontvieille Edouard , Gout Elisabeth , Guérard Florence , Bligny Richard
Published: July 2011

Day respiration is the cornerstone of nitrogen assimilation since it provides carbon skeletons to primary metabolism for glutamate (Glu) and glutamine synthesis. However, recent studies have suggested that the tricarboxylic acid pathway is rate limiting and mitochondrial pyruvate dehydrogenation is partly inhibited in the light. Pyruvate may serve as a carbon source for amino acid (e.g. alanine) or fatty acid synthesis, but pyruvate metabolism is not well documented, and neither is the possible resynthesis of phosphoenolpyruvate (PEP). Here, we examined the capacity of pyruvate to convert back to PEP using 13C and 2H labeling in illuminated cocklebur (Xanthium strumarium) leaves. We show that the intramolecular labeling pattern in Glu, 2-oxoglutarate, and malate after 13C-3-pyruvate feeding was consistent with 13C redistribution from PEP via the PEP-carboxylase reaction. Furthermore, the deuterium loss in Glu after 2H3-13C-3-pyruvate feeding suggests that conversion to PEP and back to pyruvate washed out 2H atoms to the solvent. Our results demonstrate that in cocklebur leaves, PEP resynthesis occurred as a flux from pyruvate, approximately 0.5‰ of the net CO2 assimilation rate. This is likely to involve pyruvate inorganic phosphate dikinase and the fundamental importance of this flux for PEP and inorganic phosphate homeostasis is discussed.