bluuebunny/crossref_metadata_2025 huggingface dataset:
Terahertz electroluminescence from 6Н-SiC structures with natural superlattice
Authors: Sankin V. I. , Andrianov A. V. , Zakhar`in A. O. , Petrov A. G.
Published: March 2012

We report on efficient terahertz emission in the region of 1.5-2 THz from high electric field biased 6H-SiC structures with a natural superlattice (NSL) at liquid helium temperatures. The shape of the THz emission spectrum, the linear dependence of its maximum on the bias, the characteristic field strength required to achieve the emission, and the linear polarization of the emission along the natural superlattice axis allow it to be attributed to steady-state Bloch oscillations of electrons in the 6H-SiC natural superlattice.
Multipodal coordination of a tetracarboxylic crown ether with ${\rm NH}_4^+$ NH 4+: A vibrational spectroscopy and computational study
Authors: Hurtado Paola , Gámez Francisco , Hamad Said , Martínez–Haya Bruno , Steill Jeffrey D. , Oomens Jos
Published: March 2012

The elucidation of the structural requirements for molecular recognition by the crown ether (18–crown–6)-2,3,11,12-tetracarboxylic acid (18c6H4) and its cationic complexes constitutes a topic of current fundamental and practical interest in catalysis and analytical sciences. The flexibility of the central ether ring and its four carboxyl side arms poses important challenges to experimental and theoretical approaches. In this study, infrared action vibrational spectroscopy and quantum mechanical computations are employed to characterize the conformational structure of the isolated gas phase complex formed by the 18c6H4 host with \documentclass[12pt]{minimal}\begin{document}${\rm NH}_4^+$\end{document} NH 4+ as guest. The results show that the most stable gas–phase structure is a barrel–like conformation sustained by tetrapodal H–bonding of the ammonia cation with two C=O side groups and with four oxygen atoms of the ether ring in a bifurcated arrangement. Interestingly, a similar structure had been proposed in previous crystallographic studies. The experiment also provides evidence for a significant contribution of a higher energy bowl–like conformer with features resembling those adopted by 18c6H4 in the analogous complexes with secondary amines. Such a conformation displays H−bonding between confronted side carboxyl groups and tetrapodal binding of the \documentclass[12pt]{minimal}\begin{document}${\rm NH}_4^+$\end{document} NH 4+ with the ether ring and with one C=O group. Structures involving even more extensive intramolecular H–bonding in the 18c6H4 substrate are found to lie higher in energy and are ruled out by the experiment.
Scanning tunneling microscopy reveals LiMnAs is a room temperature anti-ferromagnetic semiconductor
Authors: Wijnheijmer A. P. , Martí X. , Holý V. , Cukr M. , Novák V. , Jungwirth T. , Koenraad P. M.
Published: March 2012

We performed scanning tunneling microscopy and spectroscopy on a LiMnAs(001) thin film epitaxially grown on an InAs(001) substrate by molecular beam epitaxy. While the in situ cleavage exposed only the InAs(110) non-polar planes, the cleavage continued into the LiMnAs thin layer across several facets. We combined both topography and current mappings to confirm that the facets correspond to LiMnAs. By spectroscopy we show that LiMnAs has a band gap. The band gap evidenced in this study, combined with the known Néel temperature well above room temperature, confirms that LiMnAs is a promising candidate for exploring the concepts of high temperature semiconductor spintronics based on antiferromagnets.
Superconducting wire subject to synchronous oscillating excitations: Power dissipation, magnetic response, and low-pass filtering
Authors: Ruiz H. S. , Badía-Majós A. , Genenko Y. A. , Rauh H. , Yampolskii S. V.
Published: March 2012

Numerical simulations of a type-II superconducting wire subject to an ac transport current and oscillating transverse magnetic field are performed using the theory of the critical state. Time-dependent distributions of the current and the density of magnetic flux, the local power dissipation, and cycles of the magnetic moment are displayed. Noticeable inhomogeneous dissipation and field distortions are exposed. Results for hysteretic ac losses are reported too, and significant differences to predictions of available approximate formulae identified. Finally, a distinct low-pass filtering effect intrinsic to the wire’s magnetic response is revealed.
Resistive switching characteristics of nickel silicide layer embedded HfO2 film
Authors: Panda Debashis , Huang Chun-Yang , Tseng Tseung-Yuen
Published: March 2012

Resistive switching behavior of the Ti/HfO2:NiSi:HfO2/Pt memory structure is investigated. Auger electron spectroscopy analysis indicates no metal diffusion from the electrodes and silicide layer on high-k film. Cross-sectional transmission electron microscopic micrographs revealed the thicknesses of the HfO2 and silicide layer. Significant decrease of forming voltage is observed for the 550 °C, 1 min annealed device embedded with nickel silicide (NiSi) layers. Entire device shows bipolar switching properties with very low set/reset voltage. The optimized annealed device with NiSi embedded layer exhibits improved memory performances such as good on/off ratio (>102), long retention more than 104 s, and reasonable endurance (>103 cycles). A conducting filament model based on two stacks structure is employed to well explain the switching behaviors.
Synchronizing noncontact rack-and-pinion devices
Authors: Nasiri Mojtaba , Miri MirFaez , Golestanian Ramin
Published: March 2012

The lateral Casimir force is employed to propose a nanoscale mechanical device composed of one rack and N pinions. A coupling between the pinions via torsional springs is shown to coordinate their motion through a synchronization transition. The system can work against loads that are greater than the lateral Casimir force for each device. The existence of a stable synchronized state ensures that the system could operate in full coordination without the need of delicate fine tuning of all the characteristics such as the spring constants, the corrugation amplitudes, and the distances between the rack and the pinions.
Giant magnetoresistance in layered manganese pnictide CaMnBi2
Authors: He J. B. , Wang D. M. , Chen G. F.
Published: March 2012

We report the physical properties of a layered transition metal pnictide, CaMnBi2, which has a crystal structure similar to that of the superconducting iron pnictides. This compound is a bad metal with a long-range antiferromagnetic order at TN = 270 K. The linear temperature dependence of magnetic susceptibility above TN suggests that strong antiferromagnetic correlations exist in the paramagnetic state. A linear magnetic field dependence of the magnetoresistance implies the existence of the linear energy dispersion, which may result in the giant in-plane magnetoresistance (about 105% in 10 T at 2.5 K for H∥c). The results of de Haas-van Alphen effect are consistent with the presence of Dirac fermions.
Agglomeration defects on irradiated carbon nanotubes
Authors: Moura Cássio Stein , Balzaretti Naira Maria , Amaral Livio , Lacerda Rodrigo Gribel , Pimenta Marcos A.
Published: March 2012

Aligned carbon nanotubes (CNT) were irradiated in the longitudinal and perpendicular directions, with low energy carbon and helium ions in order to observe the formation of defects in the atomic structure. Analysis through Raman spectroscopy and scanning electron microscopy indicated bundle rupture and ion track formation on nanotube bundles. Aligned CNT presented a kind of defect comprising ravine formation and tube agglomeration on top of the substrate. The latter structure is possibly caused by static charge accumulation induced by the incoming ions. Fluence plays a role on the short range order. Higher fluence irradiation transforms CNT into amorphous carbon nanowires.
Lamb growth performance and carcass weight from rotationally grazed perennial pasture systems compared with annual pasture systems with supplements
Authors: Burnett V. F. , Seymour G. R. , Norng S. , Jacobs J. L. , Ponnampalam E. N.
Published: March 2012

Annual pastures used to finish lambs can decline in herbage nutritive value (NV) from January to April in the temperate zone. If lambs are to be finished to market specifications for carcass weight during this period, the use of summer-active perennial pastures or supplementation of annual pastures, is required. The present study investigated liveweight (LW) gain and carcass characteristics of lambs finished on perennial pastures compared with annual pastures and supplementation. Fifty-four second-cross lambs were allocated to one of the following four treatments in an asymmetric split-plot design: perennial pasture (PP), annual pasture with hay and grain (AP), AP with flaxseed (AP+FS) and AP with flaxmeal (AP+FM). Lambs were fed for 7 weeks and weighed weekly. Blood glucose and total antioxidant status were determined before, during and at the end of the experiment. Carcass weight and GR fat were measured at 24 h post-slaughter. Lambs grazing PP had significantly higher daily LW gain (P < 0.001), slaughter weight (P < 0.001), carcass weight (P < 0.01) and GR fat (total tissue depth at 12 rib, 110 mm from midline) (P < 0.001) than did lambs grazing AP, AP+FS or AP+FM. Lambs receiving AP+FS and AP+FM grew significantly faster (P < 0.001) than lambs receiving AP. It is likely that lambs grazing the perennial pasture were actively selecting the green portion of lucerne that had higher herbage NV than that indicated by the conventional feed analysis. Results show that lambs grazing a lucerne-dominant perennial pasture performed better than did lambs grazing annual pasture with supplements during the finishing period. Further work is required to determine the efficacy of other perennial species to enable economic finishing of lambs during summer and early autumn.
Contextual encoding by ensembles of medial prefrontal cortex neurons
Authors: Hyman James M. , Ma Liya , Balaguer-Ballester Emili , Durstewitz Daniel , Seamans Jeremy K.
Published: March 2012

Contextual representations serve to guide many aspects of behavior and influence the way stimuli or actions are encoded and interpreted. The medial prefrontal cortex (mPFC), including the anterior cingulate subregion, has been implicated in contextual encoding, yet the nature of contextual representations formed by the mPFC is unclear. Using multiple single-unit tetrode recordings in rats, we found that different activity patterns emerged in mPFC ensembles when animals moved between different environmental contexts. These differences in activity patterns were significantly larger than those observed for hippocampal ensembles. Whereas ≈11% of mPFC cells consistently preferred one environment over the other across multiple exposures to the same environments, optimal decoding (prediction) of the environmental setting occurred when the activity of up to ≈50% of all mPFC neurons was taken into account. On the other hand, population activity patterns were not identical upon repeated exposures to the very same environment. This was partly because the state of mPFC ensembles seemed to systematically shift with time, such that we could sometimes predict the change in ensemble state upon later reentry into one environment according to linear extrapolation from the time-dependent shifts observed during the first exposure. We also observed that many strongly action-selective mPFC neurons exhibited a significant degree of context-dependent modulation. These results highlight potential differences in contextual encoding schemes by the mPFC and hippocampus and suggest that the mPFC forms rich contextual representations that take into account not only sensory cues but also actions and time.
Crimean–Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses
Authors: Guo Yu , Wang Wenming , Ji Wei , Deng Maping , Sun Yuna , Zhou Honggang , Yang Cheng , Deng Fei , Wang Hualin , Hu Zhihong , Lou Zhiyong , Rao Zihe
Published: March 2012

Crimean–Congo hemorrhagic fever virus (CCHFV), a virus with high mortality in humans, is a member of the genus
Nairovirus
in the family
Bunyaviridae
, and is a causative agent of severe hemorrhagic fever (HF). It is classified as a biosafety level 4 pathogen and a potential bioterrorism agent due to its aerosol infectivity and its ability to cause HF outbreaks with high case fatality (∼30%). However, little is known about the structural features and function of nucleoproteins (NPs) in the
Bunyaviridae
, especially in CCHFV. Here we report a 2.3-Å resolution crystal structure of the CCHFV nucleoprotein. The protein has a racket-shaped overall structure with distinct “head” and “stalk” domains and differs significantly with NPs reported so far from other negative-sense single-stranded RNA viruses. Furthermore, CCHFV NP shows a distinct metal-dependent DNA-specific endonuclease activity. Single residue mutations in the predicted active site resulted in a significant reduction in the observed endonuclease activity. Our results present a new folding mechanism and function for a negative-strand RNA virus nucleoprotein, extend our structural insight into bunyavirus NPs, and provide a potential target for antiviral drug development to treat CCHFV infection.
Three-DOF dynamic model with lubricant contact for thermal fly-height control nanotechnology
Authors: Vakis Antonis I , Hadjicostis Christoforos N , Polycarpou Andreas A
Published: March 2012

A three-degree-of-freedom dynamic contact model with friction and lubricant contact is introduced for thermal fly-height control of a near-contact flying slider. The proposed model addresses the issue of contact with a molecularly thin lubricant layer and includes a third degree-of-freedom, roll. Neither lubricant contact nor roll has been accounted for in previous models of the head–disk interface. Roll angle rotations allow for possible contact at other slider features such as the contact pads, which may induce destabilizing moments to the slider motion and lead to unwanted slider–disk contact. While roll is important primarily during operational shock, the inclusion of lubricant contact is found to be an important determinant of the severity of steady contact while lubricant properties are shown to affect the transient properties of the jump-to- and out-of-contact slider behaviour for near- and light-contact operation. The model's validity is examined using available experimental and simulation data that predict flying height gain due to air bearing stiffening as well as significant vibration zones before and after steady-state contact.
PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction
Authors: Phan Hang T. T. , Sternberg Michael J. E.
Published: March 2012

Motivation: Analysis of protein–protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction.

Method and Results: Here we report a PPIN alignment method, called PINALOG, which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several conserved subnetworks between them that participate in similar biological processes, notably the proteasome and transcription related processes. PINALOG has been tested for its power in protein complex prediction as well as function prediction. Comparison with PSI-BLAST in predicting protein function in the twilight zone also shows that PINALOG is valuable in predicting protein function.

Availability and implementation: The PINALOG web-server is freely available from http://www.sbg.bio.ic.ac.uk/~pinalog. The PINALOG program and associated data are available from the Download section of the web-server.

Contact:  m.sternberg@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Graham Dixon-Lewis. 1 July 1922 — 5 August 2010
Authors: Bradley Derek
Published: March 2012

Graham Dixon-Lewis was a physical chemist who pioneered both experimental and mathematical studies that revealed the nature of flames. His researches, based on what was known of the chemical kinetics of hydrogen oxidation, also showed the way forward for the mathematical modelling of laminar flame structures for other fuels. These models have proved invaluable in providing the input data also for the mathematical modelling of practical turbulent flames.
Deployment of the human immunodeficiency virus type 1 protein arsenal: combating the host to enhance viral transcription and providing targets for therapeutic development
Authors: Dahiya Satinder , Nonnemacher Michael R. , Wigdahl Brian
Published: March 2012

Despite the success of highly active antiretroviral therapy in combating human immunodeficiency virus type 1 (HIV-1) infection, the virus still persists in viral reservoirs, often in a state of transcriptional silence. This review focuses on the HIV-1 protein and regulatory machinery and how expanding knowledge of the function of individual HIV-1-coded proteins has provided valuable insights into understanding HIV transcriptional regulation in selected susceptible cell types. Historically, Tat has been the most studied primary transactivator protein, but emerging knowledge of HIV-1 transcriptional regulation in cells of the monocyte–macrophage lineage has more recently established that a number of the HIV-1 accessory proteins like Vpr may directly or indirectly regulate the transcriptional process. The viral proteins Nef and matrix play important roles in modulating the cellular activation pathways to facilitate viral replication. These observations highlight the cross talk between the HIV-1 transcriptional machinery and cellular activation pathways. The review also discusses the proposed transcriptional regulation mechanisms that intersect with the pathways regulated by microRNAs and how development of the knowledge of chromatin biology has enhanced our understanding of key protein–protein and protein–DNA interactions that form the HIV-1 transcriptome. Finally, we discuss the potential pharmacological approaches to target viral persistence and enhance effective transcription to purge the virus in cellular reservoirs, especially within the central nervous system, and the novel therapeutics that are currently in various stages of development to achieve a much superior prognosis for the HIV-1-infected population.
Genetic analysis of a novel nidovirus from fathead minnows
Authors: Batts William N. , Goodwin Andrew E. , Winton James R.
Published: March 2012

A bacilliform virus was isolated from diseased fathead minnows (Pimephales promelas). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream (Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales. In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus. A PCR assay was developed for the identification of future FHMNV-like isolates.
CrystFEL: a software suite for snapshot serial crystallography
Authors: White Thomas A. , Kirian Richard A. , Martin Andrew V. , Aquila Andrew , Nass Karol , Barty Anton , Chapman Henry N.
Published: March 2012

In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.
MossA: a program for analyzing energy-domain Mössbauer spectra from conventional and synchrotron sources
Authors: Prescher Clemens , McCammon Catherine , Dubrovinsky Leonid
Published: March 2012

The programMossAprovides a straightforward approach to the fitting of57Fe conventional and synchrotron energy-domain Mössbauer spectra. Sites can be defined simply by mouse clicks and hyperfine parameters can be constrained to constant values, within specific ranges, and can be coupled linearly between different subspectra. The program includes a full transmission integral fit with Lorentzian line shape (conventional source) or Lorentzian-squared line shape (synchrotron source). The fitting process is graphically displayed in real time while fitting and can be interrupted at any time. Gaussian-shaped quadrupole splitting distributions for analyzing nonmagnetic amorphous materials are included.MossAis designed especially for the rapid and comprehensive analysis of complex Mössbauer spectra, made possible by its native graphical user input.
Reckoning electromagnetic principles with polarimetric measurements of anisotropic optically active crystals
Authors: Arteaga Oriol , Freudenthal John , Kahr Bart
Published: March 2012

A method is introduced to correlate electromagnetic theory and polarimetric experiments for anisotropic optically active crystals at oblique angles of incidence. It is based on the 4 × 4 algebraic descriptions of light propagation in layered anisotropic media, which can be simplified to 2 × 2 matrices when multiple reflections are disregarded. Spectroscopic Mueller matrix measurements in transmission and at oblique angles of incidence have been made on two uniaxial crystals: α-quartz and silver thiogallate. Their optical activity tensors have been spectroscopically determined using the method presented here.
Aripiprazole salts. I. Aripiprazole nitrate
Authors: Freire Eleonora , Polla Griselda , Baggio Ricardo
Published: March 2012

The crystal structure of aripiprazole nitrate (systematic name: 4-(2,3-dichlorophenyl)-1-{4-[(2-oxo-1,2,3,4-tetrahydroquinolin-7-yl)oxy]butyl}piperazin-1-ium nitrate), C23H28Cl2N3O2+·NO3−or AripH+·NO3−, is presented and the molecule compared with the aripiprazole molecules reported so far in the literature. Bond distances and angles appear very similar, except for a slight lengthening of the C—NH distances involving the protonated N atom, and the main differences are to be found in the molecular spatial arrangement (revealed by the sequence of torsion angles) and the intermolecular interactions (resulting from structural elements specific to this structure,viz. the nitrate counter-ions on one hand and the extra protons on the other hand as hydrogen-bond acceptors and donors, respectively). The result is the formation of [100] strips, laterally linked by weak π–π and C—Cl...π interactions, leading to a family of undulating sheets parallel to (010).
Implementing an X-ray validation pipeline for the Protein Data Bank
Authors: Gore Swanand , Velankar Sameer , Kleywegt Gerard J.
Published: March 2012

There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.
Use of noncrystallographic symmetry for automated model building at medium to low resolution
Authors: Wiegels Tim , Lamzin Victor S.
Published: March 2012

A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 Å or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments.
Traversing nature's danger zone: getting up close with Sumatra's volcanoes
Authors: Budd D.A. , Troll V.R. , Hilton D.R. , Freda C. , Jolis E.M. , Halldorsson S.A.
Published: March 2012

The Indonesian island of Sumatra, located in one of the most active zones of the Pacific Ring of Fire, is characterized by a chain of subduction‐zone volcanoes which extend the entire length of the island. As a group of volcanic geochemists, we embarked upon a five‐week sampling expedition to these exotic, remote, and in part explosive volcanoes (SAGE 2010; Sumatran Arc Geochemical Expedition). We set out to collect rock and gas samples from 17 volcanic centres from the Sumatran segment of the Sunda arc system, with the aim of obtaining a regionally significant sample set that will allow quantification of the respective roles of mantle versus crustal sources to magma genesis along the strike of the arc. Here we document our geological journey through Sumatra's unpredictable terrain, including the many challenges faced when working on active volcanoes in pristine tropical climes.
Ingestion by an endemic frugivore enhances seed germination of endemic plant species but decreases seedling survival of exotics
Authors: Zuël Nicolas , Griffiths Christine J. , Hector Andy , Hansen Dennis M. , Jones Carl G. , Albrecht Matthias
Published: March 2012

Aim  To test whether ingestion by endemic frugivores differentially affects the seed germination time, germination percentage and seedling survival of endemic, native and exotic fleshy fruited plant species, and to identify the principal processes and attributes driving such effects.

Location  Round Island, Mauritius.

Methods  We conducted a germination and seedling survival experiment for 3 months to test whether ingestion (gut passage and deposition in faeces) by the endemic Telfair’s skink (Leiolopisma telfairii) had a differential effect on the germination time, germination percentage and seedling survival of two endemic, four native and two exotic fleshy fruited plant species. To assess the importance of factors involved in the ingestion process, we used a factorial design with gut passage (gut‐passed vs. not gut‐passed), depulping (whole fruit vs. manually depulped seed) and the presence of faecal material (faeces vs. without faeces). In addition, the roles of species‐specific traits, seed size and deposition density (average number of seeds per faeces) were examined.

Results  Exotic species had a higher germination percentage than indigenous (native and endemic) species when not ingested. Following skink ingestion, there was no longer a difference, as ingestion enhanced germination percentage most in endemic species. The exotic species still germinated faster overall than the indigenous species, despite ingestion accelerating the germination time of endemics. However, ingestion strongly reduced seedling survival of the exotic species, while having no negative effect on the survival of indigenous seedlings. Overall, ingested indigenous seeds were more likely to germinate and the seedlings more likely to survive than ingested exotic seeds and seedlings. Seed size, deposition density and the removal of fruit pulp by either manual depulping or gut passage were important predictors of germination time, germination percentage and seedling survival.

Main conclusions  These endemic frugivores can enhance the competitiveness of endemic compared with exotic fleshy fruited plants at the critical germination and seedling establishment stage. Consequently, conservation and restoration of mutualistic endemic plant–animal interactions may be vital to mitigating the degradation of habitats invaded by exotic plants, which is of particular relevance for island ecosystems in which large numbers of endemics are threatened by exotic invaders.
The Prolactin Gene: A Paradigm of Tissue‐Specific Gene Regulation with Complex Temporal Transcription Dynamics
Authors: Featherstone K. , White M. R. H. , Davis J. R. E.
Published: March 2012

Transcription of numerous mammalian genes is highly pulsatile, with bursts of expression occurring with variable duration and frequency. The presence of this stochastic or ‘noisy’ expression pattern has been relatively unexplored in tissue systems. The prolactin gene provides a model of tissue‐specific gene regulation resulting in pulsatile transcription dynamics in both cell lines and endocrine tissues. In most cell culture models, prolactin transcription appears to be highly variable between cells, with differences in transcription pulse duration and frequency. This apparently stochastic transcription is constrained by a transcriptional refractory period, which may be related to cycles of chromatin remodelling. We propose that prolactin transcription dynamics result from the summation of oscillatory cellular inputs and by regulation through chromatin remodelling cycles. Observations of transcription dynamics in cells within pituitary tissue show reduced transcriptional heterogeneity and can be grouped into a small number of distinct patterns. Thus, it appears that the tissue environment is able to reduce transcriptional noise to enable coordinated tissue responses to environmental change. We review the current knowledge on the complex tissue‐specific regulation of the prolactin gene in pituitary and extra‐pituitary sites, highlighting differences between humans and rodent experimental animal models. Within this context, we describe the transcription dynamics of prolactin gene expression and how this may relate to specific processes occurring within the cell.
Genetic, biochemical and pathogenic diversity of Pseudomonas syringae pv. pisi strains
Authors: Martín‐Sanz A. , Pérez de la Vega M. , Murillo J. , Caminero C.
Published: March 2012

Pseudomonas syringae pv. pisi is a seedborne pathogen distributed worldwide that causes pea bacterial blight. Previous characterization of this pathogen has been carried out with relatively small and/or geographically limited samples. Here, a collection of 91 strains are examined that include strains from recent outbreaks in Spain (53 strains) and from 14 other countries, and that represent all races and the new race 8, including the type race strains. This collection was characterized on the basis of 55 nutritional tests, genetic analysis (rep‐PCR, amplification of AN3 and AN7 specific markers, and multilocus sequence typing (MLST)) and pathogenicity on the differential pea cultivars to identify races. Principal component analysis and distance dendrograms confirm the existence of two genetic lineages within this pathovar, which are clearly discriminated by the AN3/AN7 markers, rep‐PCR and MLST. Strains from races 1 and 7 amplified the AN3 marker; those from races 2, 6 and 8 amplified AN7, while strains of races 3, 4 and 5 amplified either AN3 or AN7. Nevertheless, strains were not grouped by race type by any of the genetic or biochemical tests. Likewise, there was no significant association between metabolic and/or genetic profiling and the geographical origin of the strains. The Spanish collection diversity reflects the variability found in the worldwide collection, suggesting multiple introductions of the bacteria into Spain by contaminated seed lots.
Stem cells in asexual reproduction of Enchytraeus japonensis (Oligochaeta, Annelid): Proliferation and migration of neoblasts
Authors: Sugio Mutsumi , Yoshida‐Noro Chikako , Ozawa Kaname , Tochinai Shin
Published: March 2012

Enchytraeus japonensis is a small oligochaete that reproduces mainly asexually by fragmentation (autotomy) and regeneration. As sexual reproduction can also be induced, it is a good animal model for the study of both somatic and germline stem cells. To clarify the features of stem cells in regeneration, we investigated the proliferation and lineage of stem cells in E. japonensis. Neoblasts, which have the morphological characteristics of undifferentiated cells, were found to firmly adhere to the posterior surface of septa in each trunk segment. Also, smaller neoblast‐like cells, which are designated as N‐cells in this study, were located dorsal to the neoblasts on the septa. By conducting 5‐bromo‐2′‐deoxyuridine (BrdU)‐labeling‐experiments, we have shown that neoblasts are slow‐cycling (or quiescent) in intact growing worms, but proliferate rapidly in response to fragmentation. N‐cells proliferate more actively than do neoblasts in intact worms. The results of pulse‐chase experiments indicated that neoblast and N‐cell lineage mesodermal cells that incorporated BrdU early in regeneration migrated toward the autotomized site to form the mesodermal region of the blastema, while the epidermal and intestinal cells also contributed to the blastema locally near the autotomized site. We have also shown that neoblasts have stem cell characteristics by expressing Ej‐vlg2 and by the activity of telomerase during regeneration. Telomerase activity was high in the early stage of regeneration and correlated with the proliferation activity in the neoblast lineage of mesodermal stem cells. Taken together, our results indicate that neoblasts are mesodermal stem cells involved in the regeneration of E. japonensis.
Unusual cause of neonatal rectal bleeding: Colonic intramural haematoma
Authors: Shankarnaryanan Srinivas , Hardikar Winita
Published: March 2012

Bright rectal bleeding in a neonate is most commonly due to necrotising enterocolitis, gastrointestinal infection or cows milk protein intolerance. We present here an infant who developed PR bleeding after cardiac surgery. Bleeding persisted despite presumptive treatment for the most common causes. A colonic intramural haematoma was identified on colonoscopy most likely related to anticoagulation in the setting of cardiac surgery.
High‐dose aprotinin, blood product transfusions, and short‐term outcome in neonates and infants: a pediatric cardiac surgery center experience
Authors: Bojan Mirela , Boulat Claire , Peperstraete Harlinde , Pouard Philippe
Published: March 2012

Background:  The efficacy of aprotinin, the most popular antifibrinolytic agent in congenital cardiac surgery, was still uncertain in small infants when its prophylactic use was suspended for safety reasons. The aim of this study is to describe associations between the prophylactic use of high‐dose aprotinin, the need for blood product transfusions, and short‐term outcome in neonates and infants with cardiac surgery.

Methods/materials:  This retrospective study included all patients younger than 1 year undergoing surgery with cardiopulmonary bypass through 42 months, before and after withdrawal of aprotinin. Each patient who received aprotinin was matched with a control with similar baseline and surgical characteristics, who have not received any antifibrinolytic agent. Associations between the use of aprotinin and the exposure to red blood cells, fresh frozen plasma, and platelet transfusions were estimated from a logistic regression model, and the exposure to additional transfusions from a polytomous regression model.

Results:  Matching resulted in two groups of 283 patients each, well balanced except for the priming volume and the ultrafiltration rate, larger in the aprotinin group. After adjustment for the priming volume and ultrafiltration rate, there was no significant association between the use of aprotinin, the exposure to any blood product transfusion, or the exposure to additional transfusions, the rate of re‐exploration for bleeding, and short‐term outcome. Two patients in the control group required re‐exploration for bleeding.

Conclusions:  No association was found between the prophylactic use of aprotinin, blood product transfusions, and short‐term outcome in this population of neonates and infants.
The functional genomics of an eco‐evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics
Authors: Becks Lutz , Ellner Stephen P. , Jones Laura E. , Hairston Nelson G.
Published: March 2012

Ecology Letters (2012) 15: 492–501

Feedbacks between ecological and evolutionary change may play important roles in community and ecosystem functioning, but a complete eco‐evolutionary feedback loop has not been demonstrated at the community level, and we know little about molecular mechanisms underlying this kind of eco‐evolutionary dynamics. In predator–prey (rotifer‐alga) microcosms, cyclical changes in predator abundance generated fluctuating selection for a heritable prey defence trait, cell clumping. Predator population growth was affected more by prey evolution than by changes in prey abundance, and changes in predator abundance drove further prey evolution, completing the feedback loop. Within a predator–prey cycle, genes up‐regulated as clumping declined were down‐regulated as clumping increased, and vice‐versa. Genes changing most in expression tended to be associated with defence or its cost. Expression patterns of individual genes differed greatly between consecutive cycles (often reversing direction), suggesting that a particular phenotype may be produced by several (perhaps many) different gene transcription pathways.
When serial prostate biopsy is recommended: most cancers detected are clinically insignificant
Authors: Zaytoun Osama M. , Stephenson Andrew J. , Fareed Khaled , El‐Shafei Ahmed , Gao Tianming , Levy David , Jones J. Stephen
Published: March 2012

Study Type – Disagnostic (exploratory cohort)

Level of Evidence 2b

What's known on the subject? and What does the study add?

Many patients undergo serial biopsy with a low rate of detection of prostate cancer, and the rate of detection declines as more biopsies are pursued. Furthermore, the clinical significance of detected cancer appears to decline as well. It is important to follow all possible methods to detect cancer; however, there should be a parallel consideration for the clinical value for detection of these tumours with low malignant potential.

The present study investigated in detail the total rate of cancer detection in serial biopsy and how many of these were deemed clinically insignificant. Moreover, it addressed the impact of detecting premalignant lesions on further detection of cancer in serial biopsy.

OBJECTIVE

Many patients pursue serial prostate biopsies after two consecutive negative biopsy sessions. The objective of this study is to determine the indications of serial prostate biopsy and to compare outcomes, including the risk of detecting clinically insignificant cancer using different biopsy protocols in this highly selected population.

PATIENTS AND METHODS

Most cases of prostate cancer are detected on initial or one repeat biopsy, but persistent suspicion of prostate cancer occasionally leads to serial biopsy, which we define as more than two biopsy sessions. We recently showed that transrectal saturation biopsy (sPBx) significantly increases cancer detection when compared with extended schemes (ePBx) in the initial repeat biopsy (second overall biopsy) population, and that most cases identified are clinically significant.

In the past decade, 479 men underwent 749 repeat prostate biopsies after two prior negative biopsy sessions.

The ePBx group included 347 biopsies with 10–14 cores.

The sPBx group included 402 biopsies with >20 cores.

We analysed overall cancer detection and risk of detecting clinically significant vs insignificant tumours.

RESULTS

Prostate cancer was detected in 15.9% of 749 serial biopsies, representing a cumulative prostate cancer detection rate of 24.8% (119/479 patients).

The sPBx group had a significantly higher detection rate per biopsy session (18.6% vs 12.7%, P= 0.026).

Nevertheless, most positive biopsies 75/119 (63%) revealed clinically insignificant cancer, including 74.6% of cancers detected by sPBx.

CONCLUSION

In men with two prior negative prostate biopsies, prostate cancer detection remains low regardless of clinical indication or transrectal biopsy protocol; most cancers identified are clinically insignificant, suggesting the threshold to repeat biopsy after more than one negative session should be very high.
Obesity: a disease or a biological adaptation? An update
Authors: Chaput J.‐P. , Doucet É. , Tremblay A.
Published: March 2012

Obesity is characterized by the accumulation of excess body fat and can be conceptualized as the physical manifestation of chronic energy excess. An important challenge of today's world is that our so‐called obesogenic environment is conducive to the consumption of energy and unfavourable to the expenditure of energy. The modern, computer‐dependent, sleep‐deprived, physically inactive humans live chronically stressed in a society of food abundance. From a physiological standpoint, the excess weight gain observed in prone individuals is perceived as a normal consequence to a changed environment rather than a pathological process. In other words, weight gain is a sign of our contemporary way of living or a ‘collateral damage’ in the physiological struggle against modernity. Additionally, substantial body fat loss can complicate appetite control, decrease energy expenditure to a greater extent than predicted, increase the proneness to hypoglycaemia and its related risk towards depressive symptoms, increase the plasma and tissue levels of persistent organic pollutants that promote hormone disruption and metabolic complications, all of which are adaptations that can increase the risk of weight regain. In contrast, body fat gain generally provides the opposite adaptations, emphasizing that obesity may realistically be perceived as an a priori biological adaptation for most individuals. Accordingly, prevention and treatment strategies for obesity should ideally target the main drivers or root causes of body fat gain in order to be able to improve the health of the population.
Successful Wage Concertation: The Economic Effects of Wage Pacts and Their Alternatives
Authors: Brandl Bernd
Published: March 2012

Recent debates on pacts have focused on the prerequisites for their emergence, whereas questions of their efficacy have receded into the background. In particular, systematic analyses of the effectiveness of pacts in terms of their capacity to enhance economic performance are missing. The aim of this article is therefore to assess the economic impact of pacts. As the majority of pacts concern wages, the assessment will concentrate on a comparison of the performance of pacts with alternative governance mechanisms for wage policies, that is, alternative pay‐setting modes. The findings show that when wage pacts are endowed with the ability to govern lower‐level pay determination, they are better at enhancing economic performance than other forms of coordination.
Indeterminacy and the Regulation of Task Allocation: The Shape of Support Roles in Healthcare
Authors: Kessler Ian , Heron Paul , Dopson Sue
Published: March 2012

Drawing upon Marsden's typology of employment systems, this article explores how the indeterminacy of the employment relationship is enacted and resolved in relation to the healthcare assistant (HCA), a key work role in the delivery of nursing care in a hospital setting. It suggests that the regulation of task allocation within nursing assumes a hybrid form, requiring further analysis of the influences shaping the HCA role. Based on multi‐method hospital case studies, the article distinguishes different types of HCA, explaining their emergence by reference to the interaction between organizational structure and personal agency. The article illustrates the value of Marsden's framework, and by addressing its limits in a healthcare setting seeks to develop a deeper understanding of task allocation in different workplace employment systems.
The phenomenon of ‘chronic Lyme’; an observational study
Authors: Ljøstad U. , Mygland Å.
Published: March 2012

Purposes:  To chart clinical, laboratory, and psychometric profiles in patients who attribute their complaints to chronic Lyme disease.

Methods:  We assessed the patients by clinical examination, laboratory tests, and questionnaires measuring fatigue, depression, anxiety, health‐related quality of life, hypochondriasis, and illness perceptions.

Results:  We found no evidence of ongoing Borrelia burgdorferi (Bb) infection in any of the 29 included patients using current diagnostic guidelines and an extended array of tests. Eight (28%) had other well‐defined illnesses. Twenty‐one (72%) had symptoms of unknown cause, of those six met the suggested criteria for post‐Lyme disease syndrome. Fourteen (48%) had presence of anti‐Bb antibodies. The patients had more fatigue and poorer health‐related quality of life as compared to normative data, but were not more depressed, anxious, or hypochondriacal. Their beliefs about the illness were characterized by negative expectations.

Conclusion:  Our patients, who all attributed their symptoms to chronic Lyme disease, were heterogeneous. None had evidences of persistent Bb infection, but whether current diagnostic criteria are functional in patients with longstanding complaints is controversial. Other well‐defined illnesses or sequelae from earlier Lyme disease were probable as main explanatory factor in some cases. The patients were not more depressed, anxious, or hypochondriacal than the normal population, but they had poorer health‐related quality of life, more fatigue, and negative expectations about their illness.
Foreigners and Outsiders: Exclusionist Attitudes towards Labour Migrants in Israel
Authors: Raijman Rebeca
Published: March 2012

This paper examines theoretical propositions regarding the social mechanisms that produce hostility and discriminatory attitudes towards out‐group populations. Specifically, we compare the effect of perceptions of socio‐economic and national threats, social contact and prejudice on social distance expressed towards labour migrants. To do so, we examine exclusionary views held by majority and minority groups (Jews and Arabs) towards non‐Jewish labour migrants in Israel. Data analysis is based on a survey of the adult Israeli population based on a stratified sample of 1,342 respondents, conducted in Israel in 2007. Altogether, our results show that Israelis (both Jews and Arabs) are resistant to accepting and integrating foreigners into Israeli society. Among Jews, this is because the incorporation of non‐Jews challenges the definition of Israel as a Jewish state and poses a threat to the homogeneity of the nation. Among Arabs, this is probably due to threat and competition over resources. The meanings of the findings are discussed within the unique ethno‐national context of Israeli society and in light of sociological theories on ethnic exclusionism.