bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution and targets of the relaxin‐3 innervation of the septal area in the rat
Authors: Olucha‐Bordonau Francisco E. , Otero‐García Marcos , Sánchez‐Pérez Ana M. , Núñez Ángel , Ma Sherie , Gundlach Andrew L.
Published: December 2011

Neural tracing studies have revealed that the rat medial and lateral septum are targeted by ascending projections from the nucleus incertus, a population of tegmental GABA neurons. These neurons express the relaxin‐family peptide, relaxin‐3, and pharmacological modulation of relaxin‐3 receptors in medial septum alters hippocampal theta rhythm and spatial memory. In an effort to better understand the basis of these interactions, we have characterized the distribution of relaxin‐3 fibers/terminals in relation to different septal neuron populations identified using established protein markers. Dense relaxin‐3 fiber plexuses were observed in regions of medial septum containing hippocampal‐projecting choline acetyltransferase (ChAT)‐, neuronal nitric oxide synthase (nNOS)‐, and parvalbumin (PV)‐positive neurons. In lateral septum (LS), relaxin‐3 fibers were concentrated in the ventrolateral nucleus of rostral LS and the ventral nucleus of caudal LS, with sparse labeling in the dorsolateral and medial nuclei of rostral LS, dorsal nucleus of caudal LS, and ventral portion nuclei. Relaxin‐3 fibers were also observed in the septofimbrial and triangular septal nuclei. In the medial septum, we observed relaxin‐3‐immunoreactive contacts with ChAT‐, PV‐, and glutamate decarboxylase‐67‐positive neurons that projected to hippocampus, and contacts between relaxin‐3 terminals and calbindin‐ and calretinin‐positive neurons. Relaxin‐3 colocalized with synaptophysin in nerve terminals in all septal areas, and ultrastructural analysis revealed these terminals were symmetrical and contacted spines, somata, dendritic shafts, and occasionally other axonal terminals. These data predict that this GABA/peptidergic projection modulates septohippocampal activity and hippocampal theta rhythm related to exploratory navigation, defensive and ingestive behaviors, and responses to neurogenic stressors. J. Comp. Neurol. 520:1903–1939, 2012. © 2011 Wiley Periodicals, Inc.
Direct Synthesis of ZnO Nanowires on Nanopatterned Surface by Magnetron Sputtering
Authors: El Mel Abdel‐Aziz , Buffière Marie , Massuyeau Florian , Gautron Eric , Xu Wei , Choi Chang‐Hwan , Wéry Jany , Faulques Eric , Barreau Nicolas , Tessier Pierre‐Yves
Published: December 2011

ZnO nanowire arrays parallel to the substrate are directly deposited by magnetron sputtering on the top of nanometric silicon line patterns prepared as a template. This method of synthesis is very simple and avoids the complicated steps of ZnO lithography. The nanoline template patterns are created by laser interference lithography combined with deep reactive ion etching. The assembly and the alignment of the nanowires after the deposition process are studied by scanning electron microscopy (SEM). The dimensions of the nanowires are regulated by those of the nanoline template patterns. The nanowires of 150 nm in width, 90 nm in height, 20 mm in length are fabricated especially for the study of their microstructure and photoluminescence effects. The microstructure is explored by X‐ray diffraction (XRD) and high‐resolution (HR) transmission electron microscopy (TEM). The nanowires show well‐crystallized ZnO nanograins in the hexagonal würtzite structure with a (002) preferential orientation on the (100) silicon surface. The nanowires exhibit a typical photoluminescence spectrum of ZnO.
Deletion of aquaporin‐4 changes the perivascular glial protein scaffold without disrupting the brain endothelial barrier
Authors: Eilert‐Olsen Martine , Haj‐Yasein Nadia Nabil , Vindedal Gry Fluge , Enger Rune , Gundersen Georg Andreas , Hoddevik Eystein Hellstrøm , Petersen Pétur Henry , Haug Finn‐Mogens S. , Skare Øivind , Adams Marvin E. , Froehner Stanley C. , Burkhardt John Michael , Thoren Anna E. , Nagelhus Erlend A.
Published: December 2011

Expression of the water channel aquaporin‐4 (AQP4) at the blood–brain interface is dependent upon the dystrophin associated protein complex. Here we investigated whether deletion of the Aqp4 gene affects the molecular composition of this protein scaffold and the integrity of the blood–brain barrier. High‐resolution immunogold cytochemistry revealed that perivascular expression of α‐syntrophin was reduced by 60% in Aqp4−/− mice. Additionally, perivascular AQP4 expression was reduced by 88% in α‐syn−/− mice, in accordance with earlier reports. Immunofluorescence showed that Aqp4 deletion also caused a modest reduction in perivascular dystrophin, whereas β‐dystroglycan labeling was unaltered. Perivascular microglia were devoid of AQP4 immunoreactivity. Deletion of Aqp4 did not alter the ultrastructure of capillary endothelial cells, the expression of tight junction proteins (claudin‐5, occludin, and zonula occludens 1), or the vascular permeability to horseradish peroxidase and Evans blue albumin dye. We conclude that Aqp4 deletion reduces the expression of perivascular glial scaffolding proteins without affecting the endothelial barrier. Our data also indicate that AQP4 and α‐syntrophin are mutually dependent upon each other for proper perivascular expression. © Wiley Periodicals, Inc.
The use of CO2 for reversible pH shifting, and the removal of succinic acid in a polymer‐based two‐phase partitioning bioreactor
Authors: Hepburn Adam J. , Daugulis Andrew J.
Published: December 2011

BACKGROUND: Succinic acid (SA) is an intermediate in the production of commodity chemicals, but SA bioproduction has not yet been commercialized due to end product inhibition and high product separation costs. Two‐phase partitioning bioreactors (TPPBs) can increase volumetric productivity through in situ product removal, although SA uptake by polymers requires a pH below the pKA2 of SA (4.2). It was proposed to reversibly reduce the pH with CO2 sparging for absorption of SA, followed by nitrogen stripping to allow continued bioproduction after returning to metabolic pH levels.

RESULTS: At 1 atm CO2 sparging lowered the pH of RO water to 3.8 but only to 4.75 in medium, requiring acid/base pH adjustment in subsequent experiments. Actinobacillus succinogenes was temporarily exposed to pH 4.2 for between 5 min and 4 h to observe the effect on subsequent growth; cells could grow after up to 4 h of low pH exposure, sufficient time for SA uptake. Because atmospheric CO2 could not adequately lower the pH of medium, a TPPB was operated with the pH being shifted using strong acid/base; SA was recovered in situ, however, the accumulation of salts hindered further cell growth.

CONCLUSION: Several key elements of this novel processing strategy were successfully demonstrated, and work is continuing with high pressure CO2 to achieve the desired pH adjustment levels. Copyright © 2011 Society of Chemical Industry
Questionnaire for impulsive‐compulsive disorders in Parkinson's Disease–Rating Scale
Authors: Weintraub Daniel , Mamikonyan Eugenia , Papay Kimberly , Shea Judith A. , Xie Sharon X. , Siderowf Andrew
Published: December 2011

Impulse control disorders and related disorders (hobbyism‐punding and dopamine dysregulation syndrome) occur in 15% to 20% of Parkinson's disease (PD) patients. We assessed the validity and reliability of the Questionnaire for Impulsive‐Compulsive Disorders in Parkinson's Disease–Rating Scale (QUIP‐RS), a rating scale designed to measure severity of symptoms and support a diagnosis of impulse control disorders and related disorders in PD. A convenience sample of PD patients at a movement disorders clinic self‐completed the QUIP‐RS and were administered a semistructured diagnostic interview by a blinded trained rater to assess discriminant validity for impulse control disorders (n = 104) and related disorders (n = 77). Subsets of patients were assessed to determine interrater reliability (n = 104), retest reliability (n = 63), and responsiveness to change (n = 29). Adequate cutoff points (both sensitivity and specificity values >80% plus acceptable likelihood ratios) were established for each impulse control disorder and hobbyism‐punding. Interrater and retest reliability (intraclass correlation coefficient r) were >0.60 for all disorders. Participants in an impulse control disorder treatment study who experienced full (t = 3.65, P = .004) or partial (t = 2.98, P = .01) response demonstrated significant improvement on the rating scale over time, while nonresponders did not (t = 0.12, P = .91). The QUIP‐RS appears to be valid and reliable as a rating scale for impulse control disorders and related disorders in PD. Preliminary results suggest that it can be used to support a diagnosis of these disorders, as well as to monitor changes in symptom severity over time. © 2011 Movement Disorder Society
Self model theory: learning from the future
Authors: Dowrick Peter W.
Published: December 2011

This paper synthesizes findings and theoretical propositions across behavioral, cognitive, and neuropsychological theories, with significant new conceptualizations bearing upon processes of learning and performance. There is a need to explain ultrarapid learning within the framework of cognitive science. In video self modeling and in challenging circumstances, the speed of behavior change appears to be derived from feedforward, in which component behaviors (in the repertoire) are reconfigured to produce a new skill or level of performance. It is argued that ‘self modeling’ is fundamental to learning, and peer/other modeling serves as an alternative. Learning in this way produces a cognitive self‐simulation which can be accessed to trigger a behavioral response in a future context. Related neurological processes are indicated by ‘mental time travel’ (MTT) and specific brain activity during the imagination (simulation) of future personal events. There is evidence that some brain mechanisms (mirror neurons), involved in immediate imitation, are differentially responsive to images of self versus other. MTT (to future events) in cognitive neuroscience has so far been discussed only in terms of prediction and planning not behavior change. These issues are brought together by self model theory. Conclusions drawn in this paper include discussions of the value in ‘learning from the future’ as a ubiquitous human ability. Overall, the propositions of this theory should stimulate diverse future research, linking neurological and behavioral contributions to cognitive science. WIREs Cogn Sci 2012, 3:215–230. doi: 10.1002/wcs.1156

This article is categorized under:

Psychology > Learning
Propionic acidemia: neonatal versus selective metabolic screening
Authors: Grünert S. C. , Müllerleile S. , de Silva L. , Barth M. , Walter M. , Walter K. , Meissner T. , Lindner M. , Ensenauer R. , Santer R. , Bodamer O. A. , Baumgartner M. R. , Brunner‐Krainz M. , Karall D. , Haase C. , Knerr I. , Marquardt T. , Hennermann J. B. , Steinfeld R. , Beblo S. , Koch H. G. , Konstantopoulou V. , Scholl‐Bürgi S. , van Teeffelen‐Heithoff A. , Suormala T. , Sperl W. , Kraus J. P. , Superti‐Furga A. , Schwab K. O. , Sass J. O.
Published: December 2011

Background

Whereas propionic acidemia (PA) is a target disease of newborn screening (NBS) in many countries, it is not in others. Data on the benefit of NBS for PA are sparse.

Study design

Twenty PA patients diagnosed through NBS were compared to 35 patients diagnosed by selective metabolic screening (SMS) prompted by clinical findings, family history, or routine laboratory test results. Clinical and biochemical data of patients from 16 metabolic centers in Germany, Austria, and Switzerland were evaluated retrospectively. Additionally, assessment of the intelligent quotient (IQ) was performed. In a second step, the number of PA patients who have died within the past 20 years was estimated based on information provided by the participating metabolic centers.

Results

Patients diagnosed through NBS had neither a milder clinical course regarding the number of metabolic crises nor a better neurological outcome. Among NBS patients, 63% were already symptomatic at the time of diagnosis, and <10% of all patients remained asymptomatic. Among all PA patients, 76% were found to be at least mildly mentally retarded, with an IQ <69. IQ was negatively correlated with the number of metabolic decompensations, but not simply with the patients’ age. Physical development was also impaired in the majority of patients. Mortality rates tended to be lower in NBS patients compared with patients diagnosed by SMS.

Conclusion

Early diagnosis of PA through NBS seems to be associated with a lower mortality rate. However, no significant benefit could be shown for surviving patients with regard to their clinical course, including the number of metabolic crises, physical and neurocognitive development, and long‐term complications.
Mission-oriented middleware for sensor-driven scientific systems
Authors: Dearle Alan , Dobson Simon
Published: December 2011

Coordinating the networks needed for modern scientific data collection and control presents a significant challenge: they are typically power- and resource-constrained, operating in noisy and hostile environments, and need to adapt their behaviour to match their operation to their sensed environment while maintaining the scientific integrity of their observations. In this paper, we explore several aspects of managing and coordinating sensor-driven systems. We draw some conclusions about how to design, structure, and implement programming and middleware abstractions for long-lived and adaptive sensor networks.
The association of parental fatal and non-fatal suicidal behaviour with offspring suicidal behaviour and depression: a systematic review and meta-analysis
Authors: Geulayov G. , Gunnell D. , Holmen T. L. , Metcalfe C.
Published: December 2011

Background

Children whose parents die by, or attempt, suicide are believed to be at greater risk of suicidal behaviours and affective disorders. We systematically reviewed the literature on these associations and, using meta-analysis, estimated the strength of associations as well as investigated potential effect modifiers (parental and offspring gender, offspring age).

Method

We comprehensively searched the literature (Medline, PsycINFO, EMBASE, Web of Science), finding 28 articles that met our inclusion criteria, 14 of which contributed to the meta-analysis. Crude odds ratio and adjusted odds ratio (aOR) were pooled using fixed-effects models.

Results

Controlling for relevant confounders, offspring whose parents died by suicide were more likely than offspring of two living parents to die by suicide [aOR 1.94, 95% confidence interval (CI) 1.54–2.45] but there were heterogeneous findings in the two studies investigating the impact on offspring suicide attempt (aOR 1.31, 95% CI 0.73–2.35). Children whose parents attempted suicide were at increased risk of attempted suicide (aOR 1.95, 95% CI 1.48–2.57). Limited evidence indicated that exposure to parental death by suicide is associated with subsequent risk of affective disorders. Maternal suicidal behaviour and younger age at exposure were associated with larger effect estimates but there was no evidence that the association differed in sons versus daughters.

Conclusions

Parental suicidal behaviour is associated with increased risk of offspring suicidal behaviour. Findings suggest that maternal suicidal behaviour is a more potent risk factor than paternal, and that children are more vulnerable than adolescents and adults. However, there is no evidence of a stronger association in either male or female offspring.
Levinas's faithfulness to Husserl, phenomenology, and God
Authors: FINEGAN THOMAS
Published: December 2011

The contemporary debate in phenomenology concerning the ‘theological turn’ raises the issue of the relationship between faith and reason. One of the foremost statements on the theological turn, that of Dominique Janicaud, is an affirmation of the faith–reason dichotomy in the context of phenomenology, specifically in relation to how thinkers like Emmanuel Levinas have abused the phenomenological project of its founder, Edmund Husserl. This article challenges the faith–reason dichotomy and shows that the role of faith in Levinas need not mark him out as a deviant from Husserlian phenomenology.
Making crime pay in late eighteenth-century Bristol: stolen goods, the informal economy and the negotiation of risk
Authors: NEALE MATT
Published: December 2011

This article examines the many ways that stolen goods were sold and circulated in late eighteenth-century Bristol. It argues that while historians have been correct to identify the contemporary importance of second-hand markets and the ‘informal economy’ to the sale of stolen property, some of the ways that stolen goods markets have been described and conceptualised are not fully supported by the evidence from Bristol. This raises questions about the extent to which models of crime based on London can be applied to cities in provincial England. The article also examines the influence that timing, appearance and location had on the way that stolen goods were sold.
Blue and green are frequently seen: responses of seeds to short- and mid-wavelength light
Authors: Goggin Danica E. , Steadman Kathryn J.
Published: December 2011

Seeds have long been a model system for studying the intricacies of phytochrome-mediated light perception and signalling. However, very little is known about how they perceive blue and green light. Cryptochromes and phototropins, the major blue-light receptors in plants, are increasingly well-studied in vegetative tissues, but their role in light perception in seeds largely remains a mystery. Green light elicits a number of responses in plants that cannot be explained by the action of any of the known photoreceptors, and some seeds are apparently also capable of perceiving green light. Here, the responses of seeds to blue and green light are collated from a thorough examination of the literature and considered from the perspective of the potential photoreceptor(s) mediating them. Knowledge of how seeds perceive wavelengths that are suboptimal for phytochrome activation could help to improve germination and seedling establishment for both crop and native species.
Local time‐dependent Pi2 frequencies confirmed by simultaneous observations from THEMIS probes in the inner magnetosphere and at low‐latitude ground stations
Authors: Kwon H.‐J. , Kim K.‐H. , Lee D.‐H. , Takahashi K. , Angelopoulos V. , Lee E. , Jin H. , Park Y.‐D. , Lee J. , Sutcliffe P. R. , Auster H. U.
Published: December 2011

Using electric and magnetic field data from Time History of Events and Macroscale Interactions during Substorms (THEMIS) fast mode waves away from midnight. probes (TH‐A, TH‐D, and TH‐E) acquired in the inner magnetosphere (L < 4) and low‐latitude ground magnetic field data from Bohyun (BOH, L = 1.35) and Hermanus (HER, L = 1.83) stations, we studied longitudinal variations of Pi2‐associated fast mode waves away from midnight. We selected 48 nightside Pi2 events at BOH identified when THEMIS probes were in the inner magnetosphere for 1 month (February 2008). During that period the probes were located between 4.0 and 20.0 magnetic local time (MLT), i.e., at and on either side of the dayside sector. This choice was motivated by our interest in studying loss of Pi2 wave energy away from its nominal source at the nightside, all the way to the dayside. Between 4.0 and 8.0 MLT the probes often observed poloidal oscillations in space during BOH Pi2 events. The poloidal oscillations had high coherence (>0.6) with BOH Pi2s and radially standing fast mode structures. Thus, these fast mode waves are explained by plasmaspheric resonance. On the duskside, however, few events at THEMIS probes had high coherence with BOH Pi2s. Furthermore, the THEMIS probe data showed no evidence of Pi2 signals at 9.0–18.0 MLT, which is consistent with previous studies. Most of the high‐coherence events were detected when the local time separation between the THEMIS probes and BOH was less than 3 h. These observations suggest that Pi2 wave energy is lost as it propagates azimuthally from a source region localized in longitude. From longitudinally separated simultaneous multipoint observations at THEMIS probes and BOH and HER stations, we found that the Pi2 frequency varies with longitude both in space and on the ground. This implies that although plasmaspheric fast mode waves establish a standing wave structure on a given meridional plane, their frequency changes with longitude if the plasmasphere is not axisymmetric. Finally, we show that a low‐latitude daytime Pi2 is not a fast mode wave propagating to the dayside through the magnetosphere.
The role of surface characteristics on intermittency and zero‐crossing properties of atmospheric turbulence
Authors: Cava Daniela , Katul Gabriel George , Molini Annalisa , Elefante Cosimo
Published: December 2011

Clustering and intermittency in atmospheric turbulent flows above different natural surfaces are investigated with reference to their dependency on surface roughness and thermal stratification. The dualism between active and quiescent phases within measured time series is isolated by using the telegraphic approximation (TA), which is able to eliminate the contributions to intermittency originating from amplitude variability associated with the energetic states. The presence of linear correlation relating the scaling exponents of energy spectra for the original series (n) and its TA counterpart (m) within the inertial sub‐range (ISR) suggests that amplitude variability acts as a de‐correlation factor for the series. Clustering exponents α estimated from velocity and scalar time series exhibit a weak dependence on the Taylor micro‐scale Reynolds number (Reλ). The average values of intermittency exponents for the original (μs) and the TA series (μTA) are linearly correlated to α for longitudinal velocity and scalars. The derived relationships shows that in the atmospheric surface layer (ASL), amplitude intermittency plays a smoothing role on the clusterization of events. On the other hand, within the canopy sublayer (CSL) above canopies, scalars are more clustered and amplitude excursions tend to amplify (or not alter) clusterization. Moreover, reducing surface roughness results in a de‐correlation between α and μTA for the vertical velocity component. Additionally, the probability density functions of inter‐pulse periods (Ip) were shown to be well approximated by the law p(Ip) ∼ Ip−γ for Ip within the ISR when γ ≈ 3 − m, which also holds for sand pile models of self organized criticality in the large pile limit.
Bacterial cis-2-unsaturated fatty acids found in the cystic fibrosis airway modulate virulence and persistence of Pseudomonas aeruginosa
Authors: Twomey Kate B , O'Connell Oisin J , McCarthy Yvonne , Dow J Maxwell , O'Toole George A , Plant Barry J , Ryan Robert P
Published: December 2011

There is an increasing appreciation of the polymicrobial nature of many bacterial infections such as those associated with cystic fibrosis (CF) and of the potentially important role for interspecies interactions in influencing both bacterial virulence and response to therapy. Patients with CF are often co-infected with Pseudomonas aeruginosa and other pathogens including Burkholderia cenocepacia and Stenotrophomonas maltophilia. These latter bacteria produce signal molecules of the diffusible signal factor (DSF) family, which are cis-2-unsaturated fatty acids. We have previously shown by in vitro studies that DSF from S. maltophilia leads to altered biofilm formation and increased resistance to antibiotics by P. aeruginosa; these responses of P. aeruginosa require the sensor kinase PA1396. Here we show that DSF signals are present in sputum taken from patients with CF. Presence of these DSF signals was correlated with patient colonization by S. maltophilia and/or B. cenocepacia. Analysis of 50 clinical isolates of P. aeruginosa showed that each responded to the presence of synthetic DSF by increased antibiotic resistance and these strains demonstrated little sequence variation in the PA1396 gene. In animal experiments using CF transmembrane conductance regulator knockout mice, the presence of DSF promoted P. aeruginosa persistence. Furthermore, antibiotic resistance of P. aeruginosa biofilms grown on human airway epithelial cells was enhanced in the presence of DSF. Taken together, these data provide substantial evidence that interspecies DSF-mediated bacterial interactions occur in the CF lung and may influence the efficacy of antibiotic treatment, particularly for chronic infections involving persistence of bacteria.
Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils
Authors: Zhang Li-Mei , Hu Hang-Wei , Shen Ju-Pei , He Ji-Zheng
Published: December 2011

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. 13CO2-DNA-stable isotope probing results showed significant assimilation of 13C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO2 fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active 13CO2-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.
Existence of ground states of hydrogen-like atoms in relativistic quantum electrodynamics. II. The no-pair operator
Authors: Könenberg Martin , Matte Oliver , Stockmeyer Edgardo
Published: December 2011

We consider a hydrogen-like atom in a quantized electromagnetic field which is modeled by means of a no-pair operator acting in the positive spectral subspace of the free Dirac operator minimally coupled to the quantized vector potential. We prove that the infimum of the spectrum of the no-pair operator is an evenly degenerate eigenvalue. In particular, we show that the bottom of its spectrum is strictly less than its ionization threshold. These results hold true, for arbitrary values of the fine-structure constant and the ultraviolet cut-off and for all Coulomb coupling constants less than the critical one of the Brown-Ravenhall model, 2/(2/π + π/2). For Coulomb coupling constants larger than the critical one, we show that the quadratic form of the no-pair operator is unbounded below. Along the way we discuss the domains and operator cores of the semi-relativistic Pauli-Fierz and no-pair operators, for Coulomb coupling constants less than or equal to the critical ones.
Optical properties and thermal response of copper films induced by ultrashort-pulsed lasers
Authors: Ren Yunpeng , Chen J. K. , Zhang Yuwen
Published: December 2011

A critical point model with three Lorentzian terms for interband transition was proposed to describe temperature-dependent reflectivity (R) and absorption coefficient (α) for copper irradiated by ultrashort-pulsed lasers of wavelength 200–1000 nm. After validated with experimental data at room temperature, it was incorporated into a two-temperature model to study ultrafast laser-material interactions. The dynamic changes of optical properties R and α, distributions of laser heat density, electron and lattice temperature, and phase changes of a copper film were investigated. Comparing with the experimental data of average absorption showed that the proposed two-temperature model together with the critical point model can simulate satisfying results for temperature-dependent R and α. The drastic changes in R and α could alter laser energy deposition in a heated target, leading to different thermal responses than those predicted with constant R and α at room temperature.
Topological origin of stretched exponential relaxation in glass
Authors: Potuzak Marcel , Welch Roger C. , Mauro John C.
Published: December 2011

The physical origin of stretched exponential relaxation is considered by many as one of the oldest unsolved problems in science. The functional form for stretched exponential relaxation can be deduced from the axiomatic diffusion-trap model of Phillips. The model predicts a topological origin for the dimensionless stretching exponent, with two “magic” values emerging: β = 3/5 arising from short-range molecular relaxation pathways and β = 3/7 for relaxation dominated by longer-range interactions. In this paper, we report experimental confirmation of these values using microscopically homogeneous silicate glass specimens. Our results reveal a bifurcation of the stretching exponent, with β = 3/5 for stress relaxation and β = 3/7 for structural relaxation, both on macroscopic length scales. These results point to two fundamentally different mechanisms governing stress relaxation versus structural relaxation, corresponding to different effective dimensionalities in configuration space during the relaxation process.
On the “U-shaped” continuum of band edge states at the Si/SiO2 interface
Authors: Ryan J. T. , Southwick R. G. , Campbell J. P. , Cheung K. P. , Young C. D. , Suehle J. S.
Published: December 2011

The historical and near universal acceptance that a U-shaped continuum of band edge states intrinsically exists at the Si/SiO2 boundary is re-examined. Using a recently developed interface defect spectroscopy method, we show that the U-shape continuum of band edge states does not exist in high quality Si/SiO2 interfaces. We then show that the U-shape continuum of band edge state can be readily measured in relatively poor quality devices, proving that the absence of states in the high quality sample is not due to measurement limitations. This observation calls into question firmly established beliefs about the intrinsic nature of the continuum.
X-ray reciprocal space mapping of dislocation-mediated strain relaxation during InGaAs/GaAs(001) epitaxial growth
Authors: Sasaki Takuo , Suzuki Hidetoshi , Takahasi Masamitu , Ohshita Yoshio , Kamiya Itaru , Yamaguchi Masafumi
Published: December 2011

Dislocation-mediated strain relaxation during lattice-mismatched InGaAs/GaAs(001) heteroepitaxy was studied through in situ x-ray reciprocal space mapping (in situ RSM). At the synchrotron radiation facility SPring-8, a hybrid system of molecular beam epitaxy and x-ray diffractometry with a two-dimensional detector enabled us to perform in situ RSM at high-speed and high-resolution. Using this experimental setup, four results in terms of film properties were simultaneously extracted as functions of film thickness. These were the lattice constants, the diffraction broadenings along in-plane and out-of-plane directions, and the diffuse scattering. Based on correlations among these results, the strain relaxation processes were classified into four thickness ranges with different dislocation behavior. In addition, the existence of transition regimes between the thickness ranges was identified. Finally, the dominant dislocation behavior corresponding to each of the four thickness ranges and transition regimes was noted.
Ferroelectric phase transition and low-temperature dielectric relaxations in Sr4(La1−xSmx)2Ti4Nb6O30 ceramics
Authors: Li Zhu Xiao , Bai Yang , Liu Xiao Qiang , Ming Chen Xiang
Published: December 2011

Ferroelectric transition and the low-temperature dielectric relaxations were investigated in Sr4(La1−xSmx)2Ti4Nb6O30 ceramics. The dielectric nature of the present ceramics was governed by the radius difference between A1- and A2-site ions. Low-temperature dielectric relaxations were indicated for all the compositions, and the diffuse ferroelectric peak appeared gradually with increasing x (increasing ion radius difference between A1- and A2-sites), and it became the normal ferroelectric one for x = 1. There was no peak on the differential scanning calorimetry (DSC) curves for the compositions with x = 0, 0.25, 0.5, and 0.75, while an obvious endothermic peak was observed for x = 1. Based on the analysis of the dielectric data and the DSC results, the ferroelectric transition for x = 1 was determined as a first order phase transition, and the second order phase transition was suggested for other compositions.
Abductions, kidnappings and killings in the Sahel and Sahara
Authors: Graham Franklin
                      Charles
Published: December 2011

Hostage-takings in North and West Africa are nothing new. What is new is the assigning of blame to al-Qaeda in the Islamic Maghreb (AQIM) and the level of resources Western powers commit to fighting AQIM and other extremists in the region. History shows that the simplified ill-defined fear of a united Islamic front against the West was unfounded. Today, however, Westerners continue to view the motivations behind such actions without considering three fundamental issues. First, who should, or can, effectively ‘govern’ the Sahara and its fringes. Second, by defining the problems as a rising pan-Islamic front, the implementation of hard-power tactics is not questioned. Finally, any consideration of the long-term disparities in the region is postponed in lieu of dealing with hostage-takings or attacks on Western targets. In reality the Sahara and Sahel are contested territories. Ideological and personal divisions are numerous. AQIM and other Jihadi Salafist movements are not popular with the regions' inhabitants. Most practice Sufi forms of Islam which are distant from such extremism. There is little attention to identifying the problems of poverty, creating state integration, and solving the problems that arise from foreign intervention. With the agenda of national leaders and/or international actors focusing on fighting terrorism or mineral resource extraction, a few inhabitants in the region kidnap foreign nationals for ideological reasons, quick money or both. The potential for hostage-taking for money is, at best, a tenuous strategy for the few.
Subtelomere-binding protein Tbf1 and telomere-binding protein Rap1 collaborate to inhibit localization of the Mre11 complex to DNA ends in budding yeast
Authors: Fukunaga Kenzo , Hirano Yukinori , Sugimoto Katsunori
Published: December 2011

Chromosome ends, known as telomeres, have to be distinguished from DNA double-strand breaks that activate DNA damage checkpoints. In budding yeast, the Mre11-Rad50-Xrs2 (MRX) complex associates with DNA ends and promotes checkpoint activation. Rap1 binds to double-stranded telomeric regions and recruits Rif1 and Rif2 to telomeres. Rap1 collaborates with Rif1 and Rif2 and inhibits MRX localization to DNA ends. This Rap1-Rif1-Rif2 function becomes attenuated at shortened telomeres. Here we show that Rap1 acts together with the subtelomere-binding protein Tbf1 and inhibits MRX localization to DNA ends. The placement of a subtelomeric sequence or TTAGGG repeats together with a short telomeric TG repeat sequence inhibits MRX accumulation at nearby DNA ends in a Tbf1-dependent manner. Moreover, tethering of both Tbf1 and Rap1 proteins decreases MRX and Tel1 accumulation at nearby DNA ends. This Tbf1- and Rap1-dependent pathway operates independently of Rif1 or Rif2 function. Depletion of Tbf1 protein stimulates checkpoint activation in cells containing short telomeres but not in cells containing normal-length telomeres. These data support a model in which Tbf1 and Rap1 collaborate to maintain genomic stability of short telomeres.
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices
Authors: Harmston Nathan , Filsell Wendy , Stumpf Michael P. H.
Published: December 2011

Motivation: The scientific literature contains a wealth of information about biological systems. Manual curation lacks the scalability to extract this information due to the ever-increasing numbers of papers being published. The development and application of text mining technologies has been proposed as a way of dealing with this problem. However, the inter-species ambiguity of the genomic nomenclature makes mapping of gene mentions identified in text to their corresponding Entrez gene identifiers an extremely difficult task. We propose a novel method, which transforms a MEDLINE record into a mixture of adjacency matrices; by performing a random walkover the resulting graph, we can perform multi-class supervised classification allowing the assignment of taxonomy identifiers to individual gene mentions. The ability to achieve good performance at this task has a direct impact on the performance of normalizing gene mentions to Entrez gene identifiers. Such graph mixtures add flexibility and allow us to generate probabilistic classification schemes that naturally reflect the uncertainties inherent, even in literature-derived data.

Results: Our method performs well in terms of both micro- and macro-averaged performance, achieving micro-F1 of 0.76 and macro-F1 of 0.36 on the publicly available DECA corpus. Re-curation of the DECA corpus was performed, with our method achieving 0.88 micro-F1 and 0.51 macro−F1. Our method improves over standard classification techniques [such as support vector machines (SVMs)] in a number of ways: flexibility, interpretability and its resistance to the effects of class bias in the training data. Good performance is achieved without the need for computationally expensive parse tree generation or ‘bag of words classification’.

Contact:  m.stumpf@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Expression of Microbiota, Toll‐like Receptors, and Their Regulators in the Small Intestinal Mucosa in Celiac Disease
Authors: Kalliomäki Marko , Satokari Reetta , Lähteenoja Hannu , Vähämiko Sanna , Grönlund Juhani , Routi Taina , Salminen Seppo
Published: December 2011

Objectives:

Less than one‐tenth of the carriers of the risk genes HLA‐DQ2 or HLA‐DQ8 develop celiac disease, suggesting that other genetic and environmental factors are important in the pathogenesis. The role of gut microbiota has been addressed previously with inconsistent findings. Our aim was to evaluate microbiota, its receptors (Toll‐like receptors [TLRs]), and regulators of the TLRs in the small intestinal mucosa in celiac disease.

Methods:

Microbiota was analyzed by quantitative polymerase chain reaction (total bacteria and 10 bacterial group‐ and species‐specific primers) and gene expression of interleukin‐8 (IL‐8), TLR2, TLR3, TLR4, TLR5, TLR9, and regulators of TLRs, Toll‐interacting protein (TOLLIP), and single immunoglobulin IL‐1R–related molecule, by relative quantitative reverse transcription‐polymerase chain reaction in 10 children with celiac disease (untreated celiacs), 9 children with normal small intestinal mucosa (controls), and 6 adults with celiac disease with normal small intestinal mucosa after following a gluten‐free diet (treated celiacs).

Results:

Small intestinal microbiota was comparable among controls, untreated celiacs, and treated celiacs. Expression of IL‐8 mRNA, a marker of intestinal inflammation, was significantly increased in untreated celiacs as compared with treated celiacs (P = 0.002) and controls (P = 0.001). Expression of TLR‐2 mRNA was significantly decreased in untreated (P = 0.001) and treated (P = 0.03) celiacs, whereas expression of TLR‐9 mRNA was increased in untreated celiacs (P = 0.001) as compared with controls. Expression of TOLLIP mRNA was downregulated in untreated celiacs as compared with controls (P = 0.02).

Conclusions:

Altered gene expression of TLR2, TLR9, and TOLLIP in small intestinal biopsies in celiac disease suggests that microbiota‐associated factors may be important in the development of the disease.
The Lesser Egyptian Jerboa,Jaculus jaculus: A Unique Rodent Model for Evolution and Development: Figure 1.
Authors: Cooper Kimberly L.
Published: December 2011

Tetrapods that have evolved the ability to run or bound at great speeds over long distances have repeatedly converged on specific morphological limb adaptations, including the loss of lateral digits, elongation of limb segments, and fusion of individual elements. Many of the more familiar cursorial animals, such as horses and deer, are large and do not lend themselves well to experimental embryonic analyses. However, a group of lesser-known bipedal rodents, the three-toed jerboas, has become an exceptional model for studying the developmental and molecular mechanisms shaping these limb morphologies. The lesser Egyptian jerboa,Jaculus jaculus, represents the most derived subfamily of jerboas and shows loss of the anterior and posterior hindlimb digits, fusion of the three central metatarsals, and dramatic elongation of the hindlimb relative to the forelimb with disproportionate elongation of the metatarsals. In addition, several unique physiological and morphological characteristics make these excellent animals for evolutionary studies. As small docile rodents, they are amenable to rearing in a laboratory setting and, along with several related species with a variety of skeletal morphologies, are plentiful enough in the wild to support field collections. The close evolutionary relationship toMus musculusand the development of genomic resources forJ. jaculussupport comparative developmental and molecular analyses.
Production of Recombinant Herpesvirus Saimiri-Based Vectors: Figure 1.
Authors: Whitehouse Adrian
Published: December 2011

Herpesvirus saimiri (HVS) is capable of infecting a range of human cell types with high efficiency. The viral genome persists as high-copy-number, circular, nonintegrated episomes that segregate to progeny upon cell division. This allows HVS-based vectors to transduce stably a dividing cell population and provide sustained transgene expression for an extended period of time both in vitro and in vivo. Moreover, the insertion of a bacterial artificial chromosome (BAC) cassette into the HVS genome simplifies the incorporation of large amounts of heterologous DNA for gene delivery. These properties offer characteristics similar to that of an artificial chromosome combined with an efficient delivery system. To insert and express a heterologous gene in an HVS-based vector, a recombinant virus must be constructed, as described in this protocol. An HVS–BAC is used to simplify and enhance the production of recombinant viruses. This requires a two-step process to insert the heterologous expression cassette first into the pHVS-Shuttle and then into the HVS–BAC.
Imaging Synaptic Inhibition with the Genetically Encoded Chloride Indicator Clomeleon
Authors: Berglund Ken , Kuner Thomas , Feng Guoping , Augustine George J.
Published: December 2011

Several techniques are available to image excitatory processes in the brain, but synaptic inhibition has remained largely invisible. Most synaptic inhibition in the brain arises from transmembrane fluxes of chloride ions (Cl−), so imaging intracellular Cl− concentration ([Cl−]i) is, in principle, a natural way to visualize the spatiotemporal dynamics of inhibition. This protocol describes the use of Clomeleon, a genetically encoded indicator of Cl−, as a tool for monitoring synaptic inhibition. It outlines procedures that can be used to image neuronal [Cl−]i in brain slices prepared from Clomeleon transgenic mice. With only minor adjustments, the same procedures should be suitable for imaging from cultured cells as well.
Forensic DNA Testing
Authors: Butler John M.
Published: December 2011

Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.
A case series of thermal scald injuries in dogs exposed to hot water from garden hoses (garden hose scalding syndrome)
Authors: Quist Erin M. , Tanabe Mika , Mansell Joanne E. K. L. , Edwards Jeffrey L.
Published: December 2011

In this report, we present a series of cases of thermal burns (scalds) in dogs resulting from exposure to hot water from a garden hose that had been lying in the sun. These dogs typically inhabited the southern and western regions of the USA, where the recorded high temperatures often exceed 32°C (90°F) during the warm summer months. Dogs with thermal scald injury in these cases presented with linear thermal burns along the dorsum, in addition to a variety of other macroscopic lesions that were dependent upon the degree of burn exposure and ranged from local erythema to ulcerated, necrotic and sloughing skin. Chronic, healed wounds were often alopecic, with markedly thickened skin and characteristically smooth and glassy scar tissue formation. Histologically, the lesions of thermal scald injury in these dogs were indistinguishable from any other second or third degree burn, and consisted of full‐thickness dermal and epidermal necrosis with occasional fibrinoid necrosis of vessel walls, vasculitis and intravascular thrombosis. Here, we closely examine 10 cases of dogs with dorsal thermal burns collected from Texas, Arizona, California, Utah, Nevada, Indiana, Michigan and North Carolina and propose the term ‘garden hose scalding syndrome (GHS)’ to describe this unique type of scald injury.
A child with BK virus infection: Inadequacy of current therapeutic strategies
Authors: Pereira Tanya , Rojas Claudia P. , Garcia‐Buitrago Monica T. , Chandar Jayanthi , Abitbol Carolyn , Seeherunvong Wacharee , Rusconi Paolo , Bruce Jocelyn H. , Zilleruelò Gaston
Published: December 2011

Pereira T, Rojas CP, Garcia‐Buitrago MT, Chandar J, Abitbol C, Seeherunvong W, Rusconi P, Bruce JH, Zilleruelò G. A child with BK virus infection: Inadequacy of current therapeutic strategies.  Pediatr Transplantation 2011. © 2011 John Wiley & Sons A/S.

Abstract:  In this report, we describe the development of BKVN in the native kidneys of a child with a cardiac transplant. Elevated BK viral DNA load by PCR necessitated a prolonged course of treatment with escalating doses of cidofovir. Despite a reduction in plasma BK viral load, the infection evolved into an invasive CNS disease, resulting in rhomboencephalitis. This case highlights the need for awareness of the possibility of developing multiorgan complications from BKV infection. The current treatment options for BKV tissue invasive disease are inadequate and need to be improved.