bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of Increased Rates of Isolation ofBacillusSpecies
Authors: Meites Elissa , Taur Ying , Marino Leslie , Schaefer Melissa , Eagan Janet , Jensen Bette , Williams Margaret , Kamboj Mini , Srinivasan Arjun
Published: October 2010

Background.

In 2007–2008, several US hospitals reported summertime increases in the number of clinical blood cultures positive forBacillusspecies, which are common environmental bacteria.

Objective.

To investigate increased rates of isolation ofBacillusspecies from blood cultures, identify risk factors, and recommend control strategies.

Design.

Survey and case-control study.

Setting.

Multiple hospitals, including a cancer center.

Methods.

We surveyed 24 facilities that reported increases. We also conducted a field investigation at a hospital with a high rate, reviewing charts, collecting clinical and environmental isolates, and observing infection control procedures. A case-control study compared inpatient case patients who had any blood culture positive forBacilluswith unmatched control patients who had a blood culture with no growth during June-August 2008.

Results.

Among surveyed facilities, mean monthly rates rose from 25 to a peak of 75Bacillus-positive blood cultures per 10,000 blood cultures performed during the period June-August. At the hospital where the case-control investigation was conducted, for most case patients (75%), theBacillus-positive blood cultures represented contamination or device colonization rather than infection. We enrolled 48 case patients and 48 control patients; in multivariate analysis, only central venous access device use was significantly associated with case status (odds ratio, 14.0;P< .01). Laboratory testing identified at least 12 differentBacillusspecies (non-anthracis) among the isolates. Observation of infection control procedures revealed variability in central line care and blood sample collection techniques.

Conclusions.

Periodic increases in the environmental load ofBacillusspecies may occur in hospitals. Our investigation indicated that at one facility, these increases likely represented a pseudo-outbreak ofBacillusspecies colonizing central venous lines or their accessories, such as needleless connector devices. Vigilant attention should be paid to infection control practices when collecting blood samples for culture, to minimize the risk of contamination by environmental microorganisms.
EVIDENCE OF QUASI-LINEAR SUPER-STRUCTURES IN THE COSMIC MICROWAVE BACKGROUND AND GALAXY DISTRIBUTION
Authors: Inoue Kaiki Taro , Sakai Nobuyuki , Tomita Kenji
Published: October 2010

Recent measurements of hot and cold spots on the cosmic microwave background (CMB) sky suggest the presence of super-structures on (>100 h
−1 Mpc) scales. We develop a new formalism to estimate the expected amplitude of temperature fluctuations due to the integrated Sachs–Wolfe (ISW) effect from prominent quasi-linear structures. Applying the developed tools to the observed ISW signals from voids and clusters in catalogs of galaxies at redshifts z < 1, we find that they indeed imply a presence of quasi-linear super-structures with a comoving radius of 100 ∼ 300 h
−1 Mpc and a density contrast |δ| ∼ O(0.1). We also find that the observed ISW signals are at odds with the concordant Λ cold dark matter model that predicts Gaussian primordial perturbations at ≳3σ level. We confirm that the mean temperature around the CMB cold spot in the southern Galactic hemisphere filtered by a compensating top-hat filter deviates from the mean value at ∼3σ level, implying that a quasi-linear supervoid or an underdensity region surrounded by a massive wall may reside at low redshifts z < 0.3 and the actual angular size (16°–17°) may be larger than the apparent size (4°–10°) discussed in literature. Possible solutions are briefly discussed.
Design and performance of domain wall displacing-type field sensors using a magnetic tunnel junction and a giant magnetoresistive device
Authors: Wang G A , Masuda Y , Kato T , Iwata S
Published: October 2010

We report a new type of field sensor, which utilizes the oscillatory domain wall displacement in the ferromagnetic free layer to detect an external field. The sensor consists of a 1200 × 100 µm2 Al conducting wire placed on a spin-valve giant magnetoresistive (GMR) or magnetic tunnel junction. By transmitting an alternating current through the Al conducting wire, an ac field can be generated to oscillate the domain wall in the free layer. The oscillatory domain wall displacement reduces the influence of wall coercivity and Barkhausen effect, and enables the sensor to detect the magnetic field which is much smaller than the wall coercivity. The field sensitivities of the domain wall displacing-type GMR and tunnel magnetoresistive (TMR) sensors are 2.73 mV V−1 Oe−1 and 5.81 mV V−1 Oe−1, respectively.
Magnetocaloric effect and magnetoresistance of Ni–Fe–Ga alloys
Authors: Pal D , Mandal K
Published: October 2010

Heusler alloys with nominal composition Ni73−x
Fe
x
Ga27 (x = 17, 18, 19, 20, 21, 22) were prepared by arc melting and subsequent homogenization by annealing. The magnetic properties of the alloys were studied to analyse the magnetic entropy change as a function of temperature. The maximum entropy change was observed in the alloy (x = 19) where martensite–austenite structural and ferro–para magnetic transitions were very close to each other. The transport properties and magnetoresistance (MR) of the samples were also investigated up to a magnetic field of 8 T and within a temperature range 4.2–325 K. It was observed that the MR in the austenite state was higher than that of the martensite state irrespective of the composition of the sample. A large negative MR (∼9% at 8 T) was obtained for the sample Ni54Fe19Ga27 at 300 K which was very close to the martensitic transition temperature as well as the Curie temperature.
Photoluminescence from a Tb-doped photonic crystal microcavity for white light generation
Authors: Li Yigang , Almeida Rui M
Published: October 2010

Terbium-doped one-dimensional triple microcavities have been prepared by sol–gel processing. The photoluminescence (PL) of Tb3+ ions outside a microcavity structure, when excited by blue laser light at 488 nm, consisted of three distinct peaks at 542, 587 and 619 nm. When embedded in the microcavities, the three Tb3+ PL peaks were enhanced, balanced and broadened by the photonic crystal structure and combined into a continuous broad band. An analysis in the CIE colour space showed that white light can be obtained by mixing the modified Tb3+ PL with the blue exciting light, while this is impossible with the original PL profile. This novel technique may improve white light generation by enhancing and modifying the spontaneous emission of current phosphors. It may also lead to the development of new rare-earth phosphor materials based on 4f–4f transitions, able to generate white light more efficiently, via simpler and cheaper alternatives to the current phosphor compositions. A novel configuration to combine this kind of structure with a white light-emitting-diode (LED) is also proposed.
Assisted electrochemical etching of photonic luminescent multilayers of porous silicon
Authors: Nava R
Published: October 2010

Porous silicon is produced by electrochemical etching of crystalline silicon substrates in an electrolyte usually composed of aqueous HF and ethanol. Under this condition, photonic multilayers can be built with highly p-type-doped (p+) substrates, or luminescent layers can be produced with lightly p-type-doped (p−) substrates. The task of building structures with both features has not been successfully achieved. In this paper, it is shown that assisted electrochemical etching of p+ substrates with polyoxometalate and H2O2 can produce multilayers with both features: luminescence in the visible region and optical quality for photonic applications.
A diffusive air plasma in bi-directional nanosecond pulsed dielectric barrier discharge
Authors: Yang De-Zheng , Wang Wen-Chun , Li Shou-Zhe , Song Ying , Nie Dong-Xia
Published: October 2010

In this study, a diffuse dielectric barrier discharge in air is generated by a bi-directional nanosecond pulsed power supply using a needle–plate electrode configuration at atmospheric pressure. Time-resolved spectra of N2(C 
3Πu → B 
3Πg, 0–0, 337.1 nm) for both positive and negative pulse discharges are recorded under severe electromagnetic interference. It is found that the lagged time of the photocurrent pulse compared with the voltage pulse in the negative pulse discharge is about 50 times longer than that in the positive pulse discharge at 16 kV pulse peak voltage and becomes shorter with an increase in pulse peak voltage. In addition, the gas temperature of the air plasma is determined to be approximately 395 K by measuring the optical emission spectra of the first negative band of
, 0–0, 391.4 nm).
Functional nanoporous structures by partial sintering of nanorod assemblies
Authors: Mukherjee B , Viswanath B , Ravishankar N
Published: October 2010

We present a general method for the synthesis of functional nanoporous structures by heat treating a loose compact of nanorods. Partial sintering of such a compact leads to spherodization of the nanorods and their fusion at the contact regions leading to an interconnected porous microstructure. The pore diameter can be controlled by changing the original nanorod diameter. We illustrate the generality of the method using TiO2, ZnO and hydroxyapatite as model systems; the method is applicable for any material that can be grown in the form of nanorods. The kinetics of the sintering process can be significantly enhanced in systems in which additional driving forces for mass transport arise from phase transitions proving an ultrafast pathway for producing biphasic porous structures. The possibility of producing hierarchical porous structures using fugitive sintering aids makes this process ideal for a variety of applications including catalysis, photoanodes for solar cells and scaffolds for biomedical applications.
Trace detection of multiwalled carbon nanotubes using Raman-enhancing silver nanocap arrays
Authors: Lang Xianzhong , Qiu Teng , Zhang Wenjun , Ji Cheng , Wang Jun , Chu Paul K
Published: October 2010

A convenient strategy is demonstrated for trace detection of multiwalled carbon nanotubes (MWNTs) using Raman-enhancing silver nanocap arrays. Microstructural analysis indicates that the hot spots are evenly distributed on the substrate. A brief analytical methodology to evaluate the dispersity of adsorbed MWNTs with different ultra-low concentrations by 2D point-by-point Raman mapping is proposed. The detection limit of this method was found to be 3 ppb. Our results open new possibilities for applying surface-enhanced Raman scattering to trace detection of an inorganic probe.
Synthesis of graphene on a polycrystalline Co film by radio-frequency plasma-enhanced chemical vapour deposition
Authors: Wang S M , Pei Y H , Wang X , Wang H , Meng Q N , Tian H W , Zheng X L , Zheng W T , Liu Y C
Published: October 2010

Graphene of 1–5 layers was synthesized on a polycrystalline Co film by radio-frequency plasma-enhanced chemical vapour deposition at a relatively low temperature of 800 °C for only 40 s in a mixture of gases of CH4/H2/Ar (1/5/20, with a total gas flow rate of 78 sccm). The obtained graphene is of high quality as revealed by Raman spectroscopy and x-ray photoelectron spectroscopy. It exhibits a high optical transmittance of more than 70% in the wavelength range 500–1200 nm, and a sheet resistivity of 2661 Ω/sq. A possible formation mechanism is proposed. The significant influence of octahedral and tetrahedral lattice interstitial sites in the Co crystallites on the formation of graphene is discussed.
Molecular dynamics simulations as a way to investigate the local physics of contact mechanics: a comparison between experimental data and numerical results
Authors: Solar M , Meyer H , Gauthier C , Benzerara O , Pelletier H , Schirrer R , Baschnagel J
Published: October 2010

In this work, a mechanical analysis of normal contact using molecular dynamics (MD) simulations is presented. Conical indentation on amorphous polymer surfaces was simulated at various temperatures and indentation rates under displacement or load control. The results are qualitatively compared with experimental data from tests on epoxy materials with different glass transition temperatures (T
g), and show good agreement with experiments. Moreover, MD simulations of nano-indentation tests allow us to estimate the mechanical properties of the polymer films studied as in experimental nano-indentation tests, which demonstrates the relevance of this approach.
Influence of UV irradiation on optical properties of thermally evaporated 4,4′-(1E, 1′E)-2,2′-(2-aminopyrimidine-4, 6-diyl)bis(ethene-2,1-diyl)bis(N,N- dimethylaniline) thin films
Authors: El-Mallah H M , El-Ghamaz N A , Waly M A
Published: October 2010

4,4′-(1E, 1′E)-2,2′-(2-aminopyrimidine-4,6-diyl)bis(ethene-2,1-diyl)bis(N,N-dimethylaniline), APBSD, was synthesized by fusing 2-amino-4,6-dimethylpyrimidine with p-N,N-dimethylaminobenzaldehyde. Thin films of APBSD were prepared by the thermal evaporation technique in a vacuum of 10−5 mbar on quartz substrates. X-ray diffraction patterns showed the amorphous nature of the thin films. Differential scanning calorimetry measurements showed no evidence of any crystallization process during heating of APBSD. Optical measurements of the as-deposited APBSD thin films showed normal dispersion of the refractive index n at λ > 800 nm and anomalous dispersion at λ < 800 nm. The results of absorption index k showed many absorption peaks in the UV region in addition to a shoulder at λ around 560 nm. The values of the lattice dielectric constant εL, the high-frequency dielectric constant ε∞, the dispersion energy E
d and the oscillator energy E
o were determined. The values of n and k were found to decrease with increasing UV-irradiation time. Absorption index patterns showed peak splitting and small changes in its position depending on the UV-irradiation time. The optical energy gap was estimated and the optical transitions were found to be indirect allowed transitions. The values of the fundamental energy gap slightly decrease, while the onset energy gap
slightly increases with increasing UV-irradiation time.
Characterization and modelling of the ion-irradiation induced disorder in 6H-SiC and 3C-SiC single crystals
Authors: Debelle A , Thomé L , Dompoint D , Boulle A , Garrido F , Jagielski J , Chaussende D
Published: October 2010

6H-SiC and 3C-SiC single crystals were simultaneously irradiated at room temperature with 100 keV Fe ions at fluences up to 4 × 1014 cm−2 (∼0.7 dpa), i.e. up to amorphization. The disordering behaviour of both polytypes has been investigated by means of Rutherford backscattering spectrometry in the channelling mode and synchrotron x-ray diffraction. For the first time, it is experimentally demonstrated that the general damage build-up is similar in both polytypes. At low dose, irradiation induces the formation of small interstitial-type defects. With increasing dose, amorphous domains start to form at the expense of the defective crystalline regions. Full amorphization of the irradiated layer is achieved at the same dose (∼0.45 dpa) for both polytypes. It is also shown that the interstitial-type defects formed during the first irradiation stage induce a tensile elastic strain (up to ∼4.0%) with which is associated an elastic energy. It is conjectured that this stored energy destabilizes the current defective microstructure observed at low dose and stimulates the formation of the amorphous nanostructures at higher dose. Finally, the disorder accumulation has been successfully reproduced with two models (namely multi-step damage accumulation and direct-impact/defect-stimulated). Results obtained from this modelling are compared and discussed in the light of experimental data.
Growth mechanism of cuboid growth pits in lead selenide epilayers grown by molecular beam epitaxy
Authors: Ma J G , Curtis M E , Zurbuchen M A , Keay J C , Weng B B , Li D H , Zhao F H , Johnson M B , Shi Z
Published: October 2010

Microstructures and crystallographic orientations of cuboid growth pits in lead selenide (PbSe) epilayers grown on Si (1 1 1) by molecular beam epitaxy (MBE) have been studied by scanning electron microscopy and cross-sectional transmission electron microscopy. Cuboid density was found to be dependent on MBE growth parameters such as sample thickness and substrate temperature. Cuboid growth defects nucleate spontaneously on the PbSe growth surface probably at Pb droplets. This nucleation results in randomly oriented PbSe crystallites that preferentially grow along the [1 0 0] axis of the NaCl-type crystal structure. This preferential growth results in cuboid crystallites with cubic faces protruding from the epitaxial (1 1 1) face.
A Novel Role of Dma1 in Regulating Forespore Membrane Assembly and Sporulation in Fission Yeast
Authors: Li Wen-zhu , Yu Zhi-yong , Ma Peng-fei , Wang Yamei , Jin Quan-wen
Published: October 2010

In fission yeast Schizosaccharomyces pombe, a diploid mother cell differentiates into an ascus containing four haploid ascospores following meiotic nuclear divisions, through a process called sporulation. Several meiosis-specific proteins of fission yeast have been identified to play essential roles in meiotic progression and sporulation. We report here an unexpected function of mitotic spindle checkpoint protein Dma1 in proper spore formation. Consistent with its function in sporulation, expression of dma1+is up-regulated during meiosis I and II. We showed that Dma1 localizes to the SPB during meiosis and the maintenance of this localization at meiosis II depends on septation initiation network (SIN) scaffold proteins Sid4 and Cdc11. Cells lacking Dma1 display defects associated with sporulation but not nuclear division, leading frequently to formation of asci with fewer spores. Our genetic analyses support the notion that Dma1 functions in parallel with the meiosis-specific Sid2-related protein kinase Slk1/Mug27 and the SIN signaling during sporulation, possibly through regulating proper forespore membrane assembly. Our studies therefore revealed a novel function of Dma1 in regulating sporulation in fission yeast.
Mps1 Phosphorylation Sites Regulate the Function of Centrin 2 in Centriole Assembly
Authors: Yang Ching-Hui , Kasbek Christopher , Majumder Shubhra , Yusof Adlina Mohd , Fisk Harold A.
Published: October 2010

The nondegradable Mps1Δ12/13protein drives centriole overproduction, suggesting that Mps1 phosphorylates a subset of centrosomal proteins to drive the assembly of new centrioles. Here we identify three Mps1 phosphorylation sites within the centriolar protein Centrin 2 (Cetn2). Although centrioles can be assembled in the absence of Cetn2, centriole assembly is attenuated in the absence of Cetn2. While wild-type Cetn2 can compensate for this attenuation, a nonphosphorylatable version cannot. In addition, overexpressing Cetn2 causes Mps1-dependent centriole overproduction that requires each of the three Mps1 phosphorylation sites within Cetn2 and is greatly exacerbated by mimicking phosphorylation at any of these sites. Wild-type Cetn2 generates excess foci that are competent as mitotic spindle poles in HsSas-6–depleted cells, suggesting that Cetn2 can organize a subset of centriolar proteins independently of cartwheels. However, centriole overproduction caused by a phosphomimetic Cetn2 mutant requires HsSas-6, suggesting that Cetn2 phosphorylation stimulates the canonical centriole assembly pathway. Moreover, in the absence of Cetn2, Mps1Δ12/13cannot drive the production of mature centrioles capable of recruiting γ-Tubulin, and a nonphosphorylatable Cetn2 mutant cannot compensate for this defect and exacerbates Cetn2 depletion. Together, our data suggest that Mps1-dependent phosphorylation of Cetn2 stimulates the canonical centriole assembly pathway.
Finding the Cell Center by a Balance of Dynein and Myosin Pulling and Microtubule Pushing: A Computational Study
Authors: Zhu Jie , Burakov Anton , Rodionov Vladimir , Mogilner Alex
Published: October 2010

The centrosome position in many types of interphase cells is actively maintained in the cell center. Our previous work indicated that the centrosome is kept at the center by pulling force generated by dynein and actin flow produced by myosin contraction and that an unidentified factor that depends on microtubule dynamics destabilizes position of the centrosome. Here, we use modeling to simulate the centrosome positioning based on the idea that the balance of three forces—dyneins pulling along microtubule length, myosin-powered centripetal drag, and microtubules pushing on organelles—is responsible for the centrosome displacement. By comparing numerical predictions with centrosome behavior in wild-type and perturbed interphase cells, we rule out several plausible hypotheses about the nature of the microtubule-based force. We conclude that strong dynein- and weaker myosin-generated forces pull the microtubules inward competing with microtubule plus-ends pushing the microtubule aster outward and that the balance of these forces positions the centrosome at the cell center. The model also predicts that kinesin action could be another outward-pushing force. Simulations demonstrate that the force-balance centering mechanism is robust yet versatile. We use the experimental observations to reverse engineer the characteristic forces and centrosome mobility.
Identification of subfamily-specific sites based on active sites modeling and clustering
Authors: de Melo-Minardi Raquel C. , Bastard Karine , Artiguenave François
Published: October 2010

Motivation: Current computational approaches to function prediction are mostly based on protein sequence classification and transfer of annotation from known proteins to their closest homologous sequences relying on the orthology concept of function conservation. This approach suffers a major weakness: annotation reliability depends on global sequence similarity to known proteins and is poorly efficient for enzyme superfamilies that catalyze different reactions. Structural biology offers a different strategy to overcome the problem of annotation by adding information about protein 3D structures. This information can be used to identify amino acids located in active sites, focusing on detection of functional polymorphisms residues in an enzyme superfamily. Structural genomics programs are providing more and more novel protein structures at a high-throughput rate. However, there is still a huge gap between the number of sequences and available structures. Computational methods, such as homology modeling provides reliable approaches to bridge this gap and could be a new precise tool to annotate protein functions.

Results: Here, we present Active Sites Modeling and Clustering (ASMC) method, a novel unsupervised method to classify sequences using structural information of protein pockets. ASMC combines homology modeling of family members, structural alignment of modeled active sites and a subsequent hierarchical conceptual classification. Comparison of profiles obtained from computed clusters allows the identification of residues correlated to subfamily function divergence, called specificity determining positions. ASMC method has been validated on a benchmark of 42 Pfam families for which previous resolved holo-structures were available. ASMC was also applied to several families containing known protein structures and comprehensive functional annotations. We will discuss how ASMC improves annotation and understanding of protein families functions by giving some specific illustrative examples on nucleotidyl cyclases, protein kinases and serine proteases.

Availability:  http://www.genoscope.fr/ASMC/.

Contact:  raquelcm@dcc.ufmg.br; kbastard@genoscope.cns.fr; artigue@genoscope.cns.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Human Carotid Body
Authors: Fagerlund Malin Jonsson , Kåhlin Jessica , Ebberyd Anette , Schulte Gunnar , Mkrtchian Souren , Eriksson Lars I.
Published: October 2010

Background

Hypoxia is a common cause of adverse events in the postoperative period, where respiratory depression due to residual effects of drugs used in anesthesia is an important underlying factor. General anesthetics and neuromuscular blocking agents reduce the human ventilatory response to hypoxia. Although the carotid body (CB) is the major oxygen sensor in humans, critical oxygen sensing and signaling pathways have been investigated only in animals so far. Thus, the aim of this study was to characterize the expression of key genes and localization of their products involved in the human oxygen sensing and signaling pathways with a focus on receptor systems and ion channels of relevance in anesthesia.

Methods

Six CBs were removed unilaterally from patients undergoing radical neck dissection. The gene expression and cell-specific protein localization in the CBs were investigated with DNA microarrays, real-time polymerase chain reaction, and immunohistochemistry.

Results

We found gene expression of the oxygen-sensing pathway, heme oxygenase 2, and the K channels TASK (TWIK-related acid sensitive K channel)-1 and BK (large-conductance potassium channel). In addition, we show the expression of critical receptor subunits such as γ-aminobutyric acid A (α2, β3, and γ2), nicotinic acetylcholine receptors (α3, α7, and β2), purinoceptors (A2A and P2X2), and the dopamine D2 receptor.

Conclusions

In unique samples of the human CB, we here demonstrate presence of critical proteins in the oxygen-sensing and signaling cascade. Our findings demonstrate similarities to, but also important differences from, established animal models. In addition, our work establishes an essential platform for studying the interaction between anesthetic drugs and human CB chemoreception.
Do I stand out or blend in? Conspicuousness awareness and consistent behavioural differences in hermit crabs
Authors: Briffa Mark , Twyman Claire
Published: October 2010

Animals titrate their behaviour against the level of risk and an individual's conspicuousness should influence decisions such as when to flee and for how long to hide. Conspicuousness will vary with variation in substrate colour. Since hermit crabs frequently change the shells they occupy, shell colour will also influence conspicuousness and to be aware of their conspicuousness would require information on both of these factors to be integrated. Reduced boldness in high-contrast shell and substrate combinations compared with situations of low contrast indicates that hermit crabs are aware of current conspicuousness. Differences between individuals remained consistent across conspicuousness levels indicating the presence of animal personalities.
Evidence for genetically influenced caste determination in phylogenetically diverse species of the termite genusReticulitermes
Authors: Kitade Osamu , Hoshi Masahiro , Odaira Shiori , Asano Akiko , Shimizu Manami , Hayashi Yoshinobu , Lo Nathan
Published: October 2010

A number of social insect species have recently been shown to have genetically influenced caste determination (GCD), challenging the conventional view that caste determination should be strictly environmental. To date, GCD has been found in phylogenetically isolated species; examples of GCD being present in multiple species of a genus are lacking. Through crossing experiments of neotenic (juvenile) reproductives, we have recently provided the first evidence for a royal versus worker GCD in the termiteReticulitermes speratus. To elucidate whether this system is more widespread, we performed crossing experiments using three additionalReticulitermesspecies. Offspring caste and sex ratios were found to be highly similar to those found previously inR. speratus, raising the possibility that GCD was present in an ancestral lineage ofReticulitermes, and subsequently maintained throughout several episodes of speciation.
Dietary protein content affects evolution for body size, body fat and viability in
Drosophila melanogaster
Authors: Kristensen Torsten N. , Overgaard Johannes , Loeschcke Volker , Mayntz David
Published: October 2010

The ability to use different food sources is likely to be under strong selection if organisms are faced with natural variation in macro-nutrient (protein, carbohydrate and lipid) availabilities. Here, we use experimental evolution to study how variable dietary protein content affects adult body composition and developmental success in
Drosophila melanogaster
. We reared flies on either a standard diet or a protein-enriched diet for 17 generations before testing them on both diet types. Flies from lines selected on protein-rich diet produced phenotypes with higher total body mass and relative lipid content when compared with those selected on a standard diet, irrespective of which of the two diets they were tested on. However, selection on protein-rich diet incurred a cost as flies reared on this diet had markedly lower developmental success in terms of egg-to-adult viability on both medium types, suggesting a possible trade-off between the traits investigated.
Unexpected resilience of species with temperature-dependent sex determination at the Cretaceous–Palaeogene boundary
Authors: Silber Sherman , Geisler Jonathan H. , Bolortsetseg Minjin
Published: October 2010

It has been suggested that climate change at the Cretaceous–Palaeogene (K–Pg) boundary, initiated by a bolide impact or volcanic eruptions, caused species with temperature-dependent sex determination (TSD), including dinosaurs, to go extinct because of a skewed sex ratio towards all males. To test this hypothesis, the sex-determining mechanisms (SDMs) of Cretaceous tetrapods of the Hell Creek Formation (Montana, USA) were inferred using parsimony optimizations of SDMs on a tree, including Hell Creek species and their extant relatives. Although the SDMs of non-avian dinosaurs could not be inferred, we were able to determine the SDMs of 62 species; 46 had genotypic sex determination (GSD) and 16 had TSD. The TSD hypothesis for extinctions performed poorly, predicting between 32 and 34 per cent of survivals and extinctions. Most surprisingly, of the 16 species with TSD, 14 of them survived into the Early Palaeocene. In contrast, 61 per cent of species with GSD went extinct. Possible explanations include minimal climate change at the K–Pg, or if climate change did occur, TSD species that survived had egg-laying behaviour that prevented the skewing of sex ratios, or had a sex ratio skewed towards female rather than male preponderance. Application of molecular clocks may allow the SDMs of non-avian dinosaurs to be inferred, which would be an important test of the pattern discovered here.
A computational study of the molecular and crystal structure and selected physical properties of octahydridosilasequioxane–(Si2O3H2)4. I. Electronic and structural aspects
Authors: Schutte C. J. H. , Pretorius J. A.
Published: October 2010

The free molecule octahydridosilasequioxane, Si8O12H8, was computationally studied, as well as embedded in the unit cell. The point group of the free molecule is indeedOh, and its crystal symmetry is reduced toC3i, thus confirming the occurrence of two different types of Si−O−Si bond lengths found experimentally. The molecular orbitals of the free molecule show that some electron density occurs in the cubic cavity, thus contributing to the opening of the Si−O−Si angle. A study of the packing in the unit cell identifies a new type of packing scheme in which eight (partial) molecules participate: each apex H atom of one protruding Si−H bond of every molecule points to the corner of anequilateraltriangle having 2.631 Å sides. All hydrogen atoms in both the free molecule and in the solid state carry negative partial charges. The reason for this is also explored, as well as its consequences for the unique packing scheme.
From phenotype to genotype: a Bayesian solution
Authors: Denwood M. J. , Mather A. E. , Haydon D. T. , Matthews L. , Mellor D. J. , Reid S. W. J.
Published: October 2010

The study of biological systems commonly depends on inferring the state of a ‘hidden’ variable, such as an underlying genotype, from that of an ‘observed’ variable, such as an expressed phenotype. However, this cannot be achieved using traditional quantitative methods when more than one genetic mechanism exists for a single observable phenotype. Using a novel latent class Bayesian model, it is possible to infer the prevalence of different genetic elements in a population given a sample of phenotypes. As an exemplar, data comprising phenotypic resistance to six antimicrobials obtained from passive surveillance ofSalmonellaTyphimurium DT104 are analysed to infer the prevalence of individual resistance genes, as well as the prevalence of a genomic island known as SGI1 and its variants. Three competing models are fitted to the data and distinguished between using posterior predictivep-values to assess their ability to predict the observed number of unique phenotypes. The results suggest that several SGI1 variants circulate in a few fixed forms through the population from which our data were derived. The methods presented could be applied to other types of phenotypic data, and represent a useful and generic mechanism of inferring the genetic population structure of organisms.
Disturbance affects short-term facilitation, but not long-term saturation, of exotic plant invasion in New Zealand forest
Authors: Spence Laura A. , Ross Joshua V. , Wiser Susan K. , Allen Robert B. , Coomes David A.
Published: October 2010

We investigate the spread of an exotic herb,Hieracium lepidulum, into a New ZealandNothofagusforest with the aim of understanding how stand-development of tree populations, propagule pressure and invader persistence, affect invasion across the landscape and within communities. Using data repeatedly collected over 35 years, from 250 locations, we parametrize continuous-time Markov chain models and use these models to examine future projections of the invasion under a range of hypothetical scenarios. We found that the probability of invasion into a stand was relatively high following canopy disturbance and that local abundance ofHieraciumwas promoted by minor disturbances. However, model predictions extrapolated 45 years into the future show that neither the rate of landscape-level invasion, nor local population growth ofHieracium, was affected much by changing the frequency of canopy disturbance events. Instead, invasion levels were strongly affected by the ability ofHieraciumto persist in the understorey following forest canopy closure, and by propagule supply from streams, forest edges and plants already established within the stand. Our results show that disturbance frequency has surprisingly little influence on the long-term trajectory of invasion, while invader persistence strongly determines invasion patterns.
Integrating species traits with extrinsic threats: closing the gap between predicting and preventing species declines
Authors: Murray Kris A. , Rosauer Dan , McCallum Hamish , Skerratt Lee F.
Published: October 2010

In studies of extinction risk, it is often insufficient to conclude that species with narrow ranges or small clutch sizes require prioritized protection. To improve conservation outcomes, we also need to know which threats interact with these traits to endanger some species but not others. In this study, we integrated the spatial patterns of key threats to Australian amphibians with species' ecological/life-history traits to both predict declining species and identify their likely threats. In addition to confirming the importance of previously identified traits (e.g. narrow range size), we find that extrinsic threats (primarily the disease chytridiomycosis and invasive mosquitofish) are equally important and interact with intrinsic traits (primarily ecological group) to create guild-specific pathways to decline in our model system. Integrating the spatial patterns of extrinsic threats in extinction risk analyses will improve our ability to detect and manage endangered species in the future, particularly where data deficiency is a problem.
Of lemmings and snowshoe hares: the ecology of northern Canada
Authors: Krebs Charles J.
Published: October 2010

Two population oscillations dominate terrestrial community dynamics in northern Canada. In the boreal forest, the snowshoe hare (Lepus americanus) fluctuates in cycles with an 8–10 year periodicity and in tundra regions lemmings typically fluctuate in cycles with a 3–4 year periodicity. I review 60 years of research that has uncovered many of the causes of these population cycles, outline areas of controversy that remain and suggest key questions to address. Lemmings are keystone herbivores in tundra ecosystems because they are a key food resource for many avian and mammalian predators and are a major consumer of plant production. There remains much controversy over the role of predation, food shortage and social interactions in causing lemming cycles. Predation is well documented as a significant mortality factor limiting numbers. Food shortage is less likely to be a major limiting factor on population growth in lemmings. Social interactions might play a critical role in reducing the rate of population growth as lemming density rises. Snowshoe hares across the boreal forest are a key food for many predators and their cycles have been the subject of large-scale field experiments that have pinpointed predation as the key limiting factor causing these fluctuations. Predators kill hares directly and indirectly stress them by unsuccessful pursuits. Stress reduces the reproductive rate of female hares and is transmitted to their offspring who also suffer reduced reproductive rates. The maternal effects produced by predation risk induce a time lag in the response of hare reproductive rate to density, aiding the cyclic dynamics.
Assassin bug uses aggressive mimicry to lure spider prey
Authors: Wignall Anne E. , Taylor Phillip W.
Published: October 2010

Assassin bugs (Stenolemus bituberus) hunt web-building spiders by invading the web and plucking the silk to generate vibrations that lure the resident spider into striking range. To test whether vibrations generated by bugs aggressively mimic the vibrations generated by insect prey, we compared the responses of spiders to bugs with how they responded to prey, courting male spiders and leaves falling into the web. We also analysed the associated vibrations. Similar spider orientation and approach behaviours were observed in response to vibrations from bugs and prey, whereas different behaviours were observed in response to vibrations from male spiders and leaves. Peak frequency and duration of vibrations generated by bugs were similar to those generated by prey and courting males. Further, vibrations from bugs had a temporal structure and amplitude that were similar to vibrations generated by leg and body movements of prey and distinctly different to vibrations from courting males or leaves, or prey beating their wings. To be an effective predator, bugs do not need to mimic the full range of prey vibrations. Instead bugs are general mimics of a subset of prey vibrations that fall within the range of vibrations classified by spiders as ‘prey’.
Geographical and temporal flexibility in the response to crosswinds by migrating raptors
Authors: Klaassen Raymond H. G. , Hake Mikael , Strandberg Roine , Alerstam Thomas
Published: October 2010

Wind and ocean currents may potentially have important effects on travelling animals, as an animal which does not respond to lateral flow will be drifted from its intended direction of movement. By analysing daily movements of migrating ospreys
Pandion haliaetus
and marsh harriers
Circus aeruginosus
, as recorded by satellite telemetry, in relation to global wind data, we showed that these raptors allow on average 47 per cent drift. Furthermore, our analyses revealed significant geographical and temporal variation in the response to crosswinds. During some parts of the migration, the birds drifted and in other parts they compensated or even overcompensated. In some regions, the response of marsh harriers depended on the wind direction. They drifted when the wind came from one side and (over)compensated when the wind came from the opposite side, and this flexible response was different in different geographical regions. These results suggest that migrating raptors modulate their response to crosswinds at different places and times during their travels and show that individual birds use a much more varied repertoire of behavioural responses to wind than hitherto assumed. Our results may also explain why contrasting and variable results have been obtained in previous studies of the effect of wind on bird migration.
Antimicrobial resistance in group B streptococcus: the Australian experience
Authors: Garland Suzanne M. , Cottrill Erin , Markowski Lisa , Pearce Chris , Clifford Vanessa , Ndisang Daniel , Kelly Nigel , Daley Andrew J.
Published: October 2010

Intrapartum chemoprophylaxis for pregnant group B streptococcus (GBS) carriers reduces vertical transmission, with a resultant decrease in neonatal as well as maternal morbidity from invasive GBS infection. Current Australian guidelines recommend penicillin for intrapartum prophylaxis of GBS carriers, with erythromycin or clindamycin for those with a β-lactam allergy. Recent reports globally suggest that resistance to erythromycin and clindamycin may be increasing; hence, a study was undertaken to promote an evidence base for local clinical guidelines. Samples collected for standardized susceptibility testing included 1160 invasive GBS isolates (264 isolates retrospectively from 1982 to 2001 and prospectively from 2002 to 2006, plus 896 prospectively collected colonizing GBS isolates gathered over a 12 month period from 2005 to 2006) from 16 laboratories around Australia. All isolates displaying phenotypic macrolide or lincosamide resistance were subsequently genotyped. No isolates showed reduced susceptibility to penicillin or vancomycin. Of the invasive isolates, 6.4 % demonstrated phenotypic erythromycin resistance and 4.2 % were clindamycin resistant. Of the erythromycin-resistant isolates, 53 % showed cross-resistance to clindamycin. Very similar results were found in colonizing specimens. There was no statistically significant change in macrolide-resistance rates over the two study periods 1982–2001 and 2002–2006. Genotyping for macrolide and lincosamide-resistant isolates was largely consistent with phenotype. These findings suggest that penicillin therapy remains an appropriate first-line antibiotic choice for intrapartum GBS chemoprophylaxis, with erythromycin and/or clindamycin resistance being low in the Australian population. It would, nevertheless, be appropriate for laboratories screening for GBS in obstetric patients to consider macrolide sensitivity testing, particularly for those with β-lactam allergy, to ensure appropriate chemoprophylaxis.
Scaffolding a Caenorhabditis nematode genome with RNA-seq
Authors: Mortazavi Ali , Schwarz Erich M. , Williams Brian , Schaeffer Lorian , Antoshechkin Igor , Wold Barbara J. , Sternberg Paul W.
Published: October 2010

Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)+ cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.
Dindel: Accurate indel calls from short-read data
Authors: Albers Cornelis A. , Lunter Gerton , MacArthur Daniel G. , McVean Gilean , Ouwehand Willem H. , Durbin Richard
Published: October 2010

Small insertions and deletions (indels) are a common and functionally important type of sequence polymorphism. Most of the focus of studies of sequence variation is on single nucleotide variants (SNVs) and large structural variants. In principle, high-throughput sequencing studies should allow identification of indels just as SNVs. However, inference of indels from next-generation sequence data is challenging, and so far methods for identifying indels lag behind methods for calling SNVs in terms of sensitivity and specificity. We propose a Bayesian method to call indels from short-read sequence data in individuals and populations by realigning reads to candidate haplotypes that represent alternative sequence to the reference. The candidate haplotypes are formed by combining candidate indels and SNVs identified by the read mapper, while allowing for known sequence variants or candidates from other methods to be included. In our probabilistic realignment model we account for base-calling errors, mapping errors, and also, importantly, for increased sequencing error indel rates in long homopolymer runs. We show that our method is sensitive and achieves low false discovery rates on simulated and real data sets, although challenges remain. The algorithm is implemented in the program Dindel, which has been used in the 1000 Genomes Project call sets.
Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
Authors: Ewing Adam D. , Kazazian Haig H.
Published: October 2010

High-throughput sequencing has recently begun to revolutionize the study of structural variants in the genomes of humans and other species. More recently, this technology and others have been applied to the study of human retrotransposon insertion polymorphisms (RIPs), yielding an unprecedented catalog of common and rare variants due to insertional mutagenesis. At the same time, the 1000 Genomes Project has released an enormous amount of whole-genome sequence data. In this article, we present evidence for 1016 L1 insertions across all studies to date that are not represented in the reference human genome assembly, many of which appear to be specific to populations or groups of populations, particularly Africans. Additionally, a cross-comparison of several studies shows that, on average, 27% of surveyed nonreference insertions is present in only one study, indicating the low frequency of many RIPs.
Neural correlates of olfactory learning: Critical role of centrifugal neuromodulation
Authors: Fletcher Max L. , Chen Wei R.
Published: October 2010

The mammalian olfactory system is well established for its remarkable capability of undergoing experience-dependent plasticity. Although this process involves changes at multiple stages throughout the central olfactory pathway, even the early stages of processing, such as the olfactory bulb and piriform cortex, can display a high degree of plasticity. As in other sensory systems, this plasticity can be controlled by centrifugal inputs from brain regions known to be involved in attention and learning processes. Specifically, both the bulb and cortex receive heavy inputs from cholinergic, noradrenergic, and serotonergic modulatory systems. These neuromodulators are shown to have profound effects on both odor processing and odor memory by acting on both inhibitory local interneurons and output neurons in both regions.