bluuebunny/crossref_metadata_2025 huggingface dataset:
Morphological priming in child German
Authors: CLAHSEN HARALD , FLEISCHHAUER ELISABETH
Published: November 2013

Regular and irregular inflection in children's production has been examined in many previous studies. Yet, little is known about the processes involved in children's recognition of inflected words. To gain insight into how children process inflected words, the current study examines regular -tand irregular -nparticiples of German using the cross-modal priming technique testing 108 monolingual German-speaking children in two age groups (group I, mean age: 8;4, group II, mean age: 9;9) and a control group of 72 adults. Although both age groups of children had the same full priming effect as adults for -tforms, only children of age group II showed an adult-like (partial) priming effect for -nparticiples. We argue that children (within the age range tested) employ the same mechanisms for regular inflection as adults but that the lexical retrieval processes required for irregular forms become more efficient when children get older.
Practical Application of Domain Analysis: Port of London Case Study
Authors: Rawson Andrew , Rogers Ed , Foster David , Phillips David
Published: November 2013

Domain analysis has a well-documented history in peer reviewed academic literature; however there are few instances of its application to facilitate the assessment of system specific navigation risk. This paper details one example of a practical approach to domain analysis for a busy section of the River Thames in Central London. The results correlate well to known high risk collision areas on the river and help to quantify and corroborate expert opinion and local knowledge. However a number of conditions must be accounted for in undertaking a robust study such as the geography of the study site, the purpose and audience of the research, and the availability of data and its limitations.
The relationships between land cover, climate and cave copepod spatial distribution and suitability along the Carpathians
Authors: MELEG IOANA NICOLETA , NĂPĂRUŞ MAGDALENA , FIERS FRANK , MELEG IONUŢ HOREA , VLAICU MARIUS , MOLDOVAN OANA TEODORA
Published: November 2013

The distribution of subterranean copepods may reflect the persistence of cave assemblages in relation to the environmental health of the overlying landscape. Areas supporting groundwater fauna were established by modelling the persistence of seven copepod species using a geographical information system (GIS). Environmental drivers were found to influence subterranean copepod distribution in the caves of the Romanian Carpathians. Habitat-based modelling, using ordinary least squares regression and geographically-weighted regression to identify the significant predictors explaining copepod habitat suitability, predicted suitable areas for the selected taxa. The most constant predictor was land cover, a measure of human impact and climate change, followed by precipitation and altitude. The model performed well for the majority of analysed taxa, and the areas predicted as suitable for narrowly distributed taxa overlapped with observed distributions. GIS facilitated the prediction of suitable habitat, and also enabled spatial autocorrelation to be tested. The results of this study demonstrate the importance of sustainable management of the terrestrial surface in limestone areas in conserving copepod biodiversity.
Morphological changes and germ layer formation in the porcine embryos from days 7–13 of development
Authors: Sun Ruizhen , Lei Lei , Liu Shichao , Xue Binghua , Wang Jianyu , Wang Jiaqiang , Shen Jingling , Duan Lian , Shen Xinghui , Cong Yimei , Gu Yanli , Hu Kui , Jin Lianhong , Liu Zhong-hua
Published: November 2013

Morphogenesis and identification of embryonic differentiation in porcine embryos are crucial issues for developmental biology and laboratory animal science. The current paper presents a study on the asynchronous development of hatched porcine embryos from days 7 to 13 post-insemination. Examination of semi-thin sections of the hypoblast showed that it had characteristics similar to those of the mouse anterior visceral endoderm during embryonic disc formation. Also, a cavity appeared in the epiblast, which was similar to a mouse proamniotic cavity. With the gradual disappearance of Rauber's layer, the cavity opened and contacted the external environment directly, all of which formed the embryonic disc. To confirm the differentiation characteristics, we performed immunohistochemical analyses and showed that GATA6 was detected clearly in parietal endoderm cells during embryonic disc establishment. OCT4 was expressed in the inner cell mass (ICM) and trophoblast of hatched blastocysts and in the epiblast during formation of the embryonic disc. However, OCT4 showed comparatively decreased expression in the posterior embryonic disc, primitive streak and migrating cells. SOX2 was present in the ICM and epiblast. Therefore, both SOX2 and OCT4 can be used as markers of pluripotent cells in the porcine embryonic disc. At the start of gastrulation, staining revealed VIMENTIN in the posterior of the embryonic disc, primitive streak and in migrating cells that underlay the embryonic disc and was also expressed in epiblast cells located in the anterior primitive streak. Together with serial sections of embryos stained by whole mount immunohistochemistry, the mesoderm differentiation pattern was shown as an ingression movement that took place at the posterior of the embryonic disc and with bilateral migration along the embryonic disc borders.
Screening of congenital heart disease in the second trimester of pregnancy: current knowledge and new perspectives to the clinical practice
Authors: Alves Rocha Luciane , Araujo Júnior Edward , Rolo Liliam Cristine , Barros Fernanda Silveira Bello , Silva Karina Peres , Martinez Luis Henrique , Nardozza Luciano Marcondes Machado , Moron Antonio Fernandes
Published: November 2013

Objective

Congenital heart diseases are common in foetuses, with an incidence greater than six times that of chromosomal abnormalities; however, experts in cardiac anatomy have evaluated only the foetuses of pregnant women with increased risk for congenital heart disease. Over the years, it has become clear that congenital heart disease occur in foetuses of low-risk women. In the mid-1980s, a proposal to expand the assessment of cardiac anatomy was presented to obstetricians in order to improve prenatal screening. With the aim to systematise and improve the diagnosis of congenital heart disease in foetuses, the International Society of Ultrasound in Obstetrics and Gynecology established an ultrasound heart examination guideline. In this review, we have described the important features of this guideline and discussed the applications of this tool in clinical practice.

Methods

We performed a literature search of the National Library of Medicine for publications released between 2000 and 2012; we used search terms pertinent to congenital heart disease, such as foetal echocardiography, foetal heart and cardiac screening examination.

Results

The guidelines serve as a standard and help to systematise the screening for congenital heart diseases, but we think that some topics may be added to design the most appropriate screening method. However, we cannot expand the topics to be evaluated in this examination without good training of sonographers who undergo this screening.

Conclusion

Although the screening standardisation is a good tool to be used in day-to-day practice, the increment of aortic and ductal archs and colour Doppler to heart screening could be useful to detect further cardiac defects.
A review of FDA-approved treatment options in bipolar depression
Authors: McIntyre Roger S. , Cha Danielle S. , Kim Rachael D. , Mansur Rodrigo B.
Published: November 2013

Objectives/Introduction

Herein we review the evidence supporting Food and Drug Administration (FDA) approved and emerging treatments for bipolar depression.

Methods

A PubMed search of all English-language articles published up to July 2013 was conducted. The search terms were quetiapine, olanzapine-fluoxetine, olanzapine, lurasidone, ketamine, modafinil/armodafinil, and lamotrigine. The search was augmented with a manual review of relevant article reference lists, as well as posters presented at national and international meetings. Articles selected for review were based on the adequacy of sample size, the use of standardized diagnostic instruments, validated assessment measures, and overall manuscript quality.

Results

Olanzapine-fluoxetine combination (OFC), quetiapine, and lurasidone are FDA-approved for the acute treatment of bipolar depression. Lurasidone is the most recently approved agent for bipolar depression. Olanzapine-fluoxetine combination and quetiapine are approved as single modality therapies while lurasidone is approved as a monotherapy and as an adjunct to lithium or divalproex. The overall effect size of the 3 treatments in mitigating depressive symptoms is similar. Clinically significant weight gain and metabolic disruption as well as sedation are significant limitations of OFC and quetiapine. The minimal propensity for weight gain as well as the metabolic neutrality of lurasidone in the bipolar population is a clinically significant advantage. Evidence also supports lamotrigine with compelling evidence as an adjunct to lithium and in recurrence prevention paradigm; suggested evidence also exists for ketamine and modafinil/armodafinil; notwithstanding, these treatments remain investigational.

Conclusion

Relatively few agents are FDA-approved for bipolar depression. The selection and sequencing of agents in bipolar depression should give primacy to those agents that are FDA-approved. Further refinement of the selection process will need to pay careful attention to the relative hazards of weight gain and metabolic disruption in this highly susceptible population. Other agents with differential mechanisms (eg, ketamine) offer a promising alternative in bipolar depression.
Cognitive and Psychosocial Phenotype of Young Children with Neurofibromatosis-1
Authors: Klein-Tasman Bonita P. , Janke Kelly M. , Luo Wen , Casnar Christy L. , Hunter Scott J. , Tonsgard James , Trapane Pamela , van der Fluit Faye , Kais Lorri A.
Published: November 2013

Children with neurofibromatosis-1 (NF1), a neurodevelopmental disorder resulting from a mutation of the NF1 gene (17q11.2), often have difficulties with learning and attention, but there is little research in the early childhood years. In this study, the cognitive and psychosocial functioning of 40 young children with NF1 (ages 3 through 6) was examined and compared both to normative data and to a contrast group comprised of unaffected siblings and community members matched for age and socio-economic status (n = 37). Children with NF1 showed significantly weaker cognitive abilities across all domains and for the vast majority of subtests. Consistent with research in older children, a variety of patterns of intra-individual strength and weakness were present for young children with NF1. Few significant group differences in psychosocial functioning were observed, but the children with NF1 showed significantly greater functional communication problems than did the unaffected group. Overall, the results indicate that in participant groups matched for age and socioeconomic status, cognitive vulnerabilities are evident for close to half of young children with NF1, with some relations to psychosocial functioning, particularly functional communication, attention problems and social skills. (JINS, 2014, 1, 1–11)
Dressed or undressed? How to measure children's body weight in overweight surveillance?
Authors: Censi Laura , Spinelli Angela , Roccaldo Romana , Bevilacqua Noemi , Lamberti Anna , Angelini Veronica , Nardone Paola , Baglio Giovanni
Published: November 2013

Objective

To simplify body weight measurement and, particularly, to encourage children and their parents to participate in the Italian nutritional surveillance system OKkio alla SALUTE, children were measured with clothes and then the weight was corrected for the estimated weight of the clothes. In the present study we compared the children's weight measured in underwear, as recommended by the WHO (WWHO), with that obtained using the OKkio alla SALUTE protocol (WOK) and investigated how the latter affects the calculation of BMI and the assessment of overweight and obesity prevalence.

Design

Weight (twice in close sequence, with and without clothing) and height were measured. A checklist was used to describe the type of clothing worn. The estimated weight of clothing was subtracted from the WOK. BMI was calculated considering both values of weight and height; ponderal status was defined using both the International Obesity Task Force and WHO BMI cut-offs.

Setting

Thirty-seven third grade classes of thirteen primary schools in Rome and in two towns in the Lazio Region were recruited.

Subjects

The anthropometric measurements were taken on 524 children aged 8–9 years.

Results

The error in the calculation of BMI from WOKwas very low, 0·005 kg/m2(95 % CI −0·185, 0·195 kg/m2); the agreement between the percentages of overweight (not including obesity) and obese children calculated with the two methods was very close to 1 (κ= 0·98).

Conclusions

The error in BMI and in nutritional classification can be considered minor in a surveillance system for monitoring overweight/obesity, but eases the procedure for measuring children.
Dietary intake assessment in women with different weight and pregnancy status using a short questionnaire
Authors: Svensson Åsa , Renström Frida , Bluck Les , Lissner Lauren , Franks Paul W , Larsson Christel
Published: November 2013

Objective

First, to evaluate the ability of a short dietary questionnaire (SDQ) to estimate energy intake (EI) on group and individual levels compared with total energy expenditure (TEE) measured by the doubly labelled water method. Second, to compare the SDQ's performance in estimating energy, nutrient and food intakes with a sixty-six-item FFQ used in large-scale Swedish epidemiological research.

Design

Cross-sectional.

Setting

Umeå, Sweden.

Subjects

In total, sixty-five non-pregnant women, of whom thirty-one were overweight or obese, and twenty-five pregnant, normal-weight women completed the protocol.

Results

On average, the SDQ captured 78 % and 79 % of absolute TEE in the non-pregnant and pregnant normal-weight women, respectively. Furthermore, the SDQ captured an average of 57 % of TEE in the overweight/obese non-pregnant women. The Spearman correlation of EI and TEE was significant in the overweight and obese women only (ρ= 0·37, 95 % CI 0·02, 0·64). There was no significant difference between the SDQ and the more extensive FFQ in the ability to assess EI when compared with TEE. Intakes of most nutrients and foods were significantly higher when assessed with the SDQ compared with the FFQ.

Conclusions

A new short dietary questionnaire with an alternative design underestimated EI of non-pregnant and pregnant, overweight and obese women on a group level but was able to rank the overweight/obese women according to EI. Furthermore, the short questionnaire captured as much or more of the energy, nutrient and food intakes of non-pregnant normal-weight and overweight/obese women on the group level as a traditional, more extensive FFQ.
Three wise centromere functions: see no error, hear no break, speak no delay
Authors: Tanaka Tomoyuki U , Clayton Lesley , Natsume Toyoaki
Published: November 2013

The main function of the centromere is to promote kinetochore assembly for spindle microtubule attachment. Two additional functions of the centromere, however, are becoming increasingly clear: facilitation of robust sister‐chromatid cohesion at pericentromeres and advancement of replication of centromeric regions. The combination of these three centromere functions ensures correct chromosome segregation during mitosis. Here, we review the mechanisms of the kinetochore–microtubule interaction, focusing on sister‐kinetochore bi‐orientation (or chromosome bi‐orientation). We also discuss the biological importance of robust pericentromeric cohesion and early centromere replication, as well as the mechanisms orchestrating these two functions at the microtubule attachment site.
Cellular dynamics in the muscle satellite cell niche
Authors: Bentzinger C Florian , Wang Yu Xin , Dumont Nicolas A , Rudnicki Michael A
Published: November 2013

Satellite cells, the quintessential skeletal muscle stem cells, reside in a specialized local environment whose anatomy changes dynamically during tissue regeneration. The plasticity of this niche is attributable to regulation by the stem cells themselves and to a multitude of functionally diverse cell types. In particular, immune cells, fibrogenic cells, vessel‐associated cells and committed and differentiated cells of the myogenic lineage have emerged as important constituents of the satellite cell niche. Here, we discuss the cellular dynamics during muscle regeneration and how disease can lead to perturbation of these mechanisms. To define the role of cellular components in the muscle stem cell niche is imperative for the development of cell‐based therapies, as well as to better understand the pathobiology of degenerative conditions of the skeletal musculature.
Mesenchymal stem cells: environmentally responsive therapeutics for regenerative medicine
Authors: Murphy Matthew B , Moncivais Kathryn , Caplan Arnold I
Published: November 2013

Mesenchymal stem cells (MSCs) are partially defined by their ability to differentiate into tissues including bone, cartilage and adipose in vitro, but it is their trophic, paracrine and immunomodulatory functions that may have the greatest therapeutic impact in vivo. Unlike pharmaceutical treatments that deliver a single agent at a specific dose, MSCs are site regulated and secrete bioactive factors and signals at variable concentrations in response to local microenvironmental cues. Significant progress has been made in understanding the biochemical and metabolic mechanisms and feedback associated with MSC response. The anti-inflammatory and immunomodulatory capacity of MSC may be paramount in the restoration of localized or systemic conditions for normal healing and tissue regeneration. Allogeneic MSC treatments, categorized as a drug by regulatory agencies, have been widely pursued, but new studies demonstrate the efficacy of autologous MSC therapies, even for individuals affected by a disease state. Safety and regulatory concerns surrounding allogeneic cell preparations make autologous and minimally manipulated cell therapies an attractive option for many regenerative, anti-inflammatory and autoimmune applications.
Three-dimensional optical holography using a plasmonic metasurface
Authors: Huang Lingling , Chen Xianzhong , Mühlenbernd Holger , Zhang Hao , Chen Shumei , Bai Benfeng , Tan Qiaofeng , Jin Guofan , Cheah Kok-Wai , Qiu Cheng-Wei , Li Jensen , Zentgraf Thomas , Zhang Shuang
Published: November 2013

Benefitting from the flexibility in engineering their optical response, metamaterials have been used to achieve control over the propagation of light to an unprecedented level, leading to highly unconventional and versatile optical functionalities compared with their natural counterparts. Recently, the emerging field of metasurfaces, which consist of a monolayer of photonic artificial atoms, has offered attractive functionalities for shaping wave fronts of light by introducing an abrupt interfacial phase discontinuity. Here we realize three-dimensional holography by using metasurfaces made of subwavelength metallic nanorods with spatially varying orientations. The phase discontinuity takes place when the helicity of incident circularly polarized light is reversed. As the phase can be continuously controlled in each subwavelength unit cell by the rod orientation, metasurfaces represent a new route towards high-resolution on-axis three-dimensional holograms with a wide field of view. In addition, the undesired effect of multiple diffraction orders usually accompanying holography is eliminated.
Efficient synthesis of manganese(ii) carboxylates: from a trinuclear cluster [Mn3(PhCO2)6(THF)4] to a unique [Mn(PhCO2)2]n chiral 3D network
Authors: Kornowicz Arkadiusz , Komorski Szymon , Wróbel Zbigniew , Justyniak Iwona , Nedelko Natalia , Ślawska-Waniewska Anna , Balawender Robert , Lewiński Janusz
Published: November 2013

The reactivity of metallic manganese towards carboxylic acids was investigated and a novel general procedure for obtaining anhydrous manganese carboxylates was developed.
A comparison and optimization of methods and factors affecting the transformation of Escherichia coli
Authors: Chan Weng-Tat , Verma Chandra S. , Lane David P. , Gan Samuel Ken-En
Published: November 2013

DNA manipulation routinely requires competent bacteria that can be made using one of numerous methods. To determine the best methods, we compared four commonly used chemical methods (DMSO, MgCl2–CaCl2, CaCl2 and Hanahan's methods) on frequently used Escherichia coli (E. coli) strains: DH5α, XL-1 Blue, SCS110, JM109, TOP10 and BL21-(DE3)-PLysS. Hanahan's method was found to be most effective for DH5α, XL-1 Blue and JM109 strains (P<0.05), whilst the CaCl2 method was best for SCS110, TOP10 and BL21 strains (P<0.05). The use of SOB (super optimal broth) over LB [Luria–Bertani (broth)] growth media was found to enhance the competency of XL-1 Blue (P<0.05), dampened JM109′s competency (P<0.05), and had no effect on the other strains (P>0.05). We found no significant differences between using 45 or 90 s heat shock across all the six strains (P>0.05). Through further optimization by means of concentrating the aliquots, we were able to get further increases in transformation efficiencies. Based on the optimized parameters and methods, these common laboratory E. coli strains attained high levels of TrE (transformation efficiency), thus facilitating the production of highly efficient and cost-effective competent bacteria.
Statins and the autonomic nervous system
Authors: Millar Philip J. , Floras John S.
Published: November 2013

Statins (3-hydroxy-3-methylglutaryl-CoA reductase inhibitors) reduce plasma cholesterol and improve endothelium-dependent vasodilation, inflammation and oxidative stress. A ‘pleiotropic’ property of statins receiving less attention is their effect on the autonomic nervous system. Increased central sympathetic outflow and diminished cardiac vagal tone are disturbances characteristic of a range of cardiovascular conditions for which statins are now prescribed routinely to reduce cardiovascular events: following myocardial infarction, and in hypertension, chronic kidney disease, heart failure and diabetes. The purpose of the present review is to synthesize contemporary evidence that statins can improve autonomic circulatory regulation. In experimental preparations, high-dose lipophilic statins have been shown to reduce adrenergic outflow by attenuating oxidative stress in central brain regions involved in sympathetic and parasympathetic discharge induction and modulation. In patients with hypertension, chronic kidney disease and heart failure, lipophilic statins, such as simvastatin or atorvastatin, have been shown to reduce MNSA (muscle sympathetic nerve activity) by 12–30%. Reports concerning the effect of statin therapy on HRV (heart rate variability) are less consistent. Because of their implications for BP (blood pressure) control, insulin sensitivity, arrhythmogenesis and sudden cardiac death, these autonomic nervous system actions should be considered additional mechanisms by which statins lower cardiovascular risk.
Mathematical model of gas plasma applied to chronic wounds
Authors: Wang J. G. , Liu X. Y. , Liu D. W. , Lu X. P. , Zhang Y. T.
Published: November 2013

Chronic wounds are a major burden for worldwide health care systems, and patients suffer pain and discomfort from this type of wound. Recently gas plasmas have been shown to safely speed chronic wounds healing. In this paper, we develop a deterministic mathematical model formulated by eight-species reaction-diffusion equations, and use it to analyze the plasma treatment process. The model follows spatial and temporal concentration within the wound of oxygen, chemoattractants, capillary sprouts, blood vessels, fibroblasts, extracellular matrix material, nitric oxide (NO), and inflammatory cell. Two effects of plasma, increasing NO concentration and reducing bacteria load, are considered in this model. The plasma treatment decreases the complete healing time from 25 days (normal wound healing) to 17 days, and the contributions of increasing NO concentration and reducing bacteria load are about 1/4 and 3/4, respectively. Increasing plasma treatment frequency from twice to three times per day accelerates healing process. Finally, the response of chronic wounds of different etiologies to treatment with gas plasmas is analyzed.
Challenges and opportunities for multi-functional oxide thin films for voltage tunable radio frequency/microwave components
Authors: Subramanyam Guru , Cole M. W. , Sun Nian X. , Kalkur Thottam S. , Sbrockey Nick M. , Tompa Gary S. , Guo Xiaomei , Chen Chonglin , Alpay S. P. , Rossetti G. A. , Dayal Kaushik , Chen Long-Qing , Schlom Darrell G.
Published: November 2013

There has been significant progress on the fundamental science and technological applications of complex oxides and multiferroics. Among complex oxide thin films, barium strontium titanate (BST) has become the material of choice for room-temperature-based voltage-tunable dielectric thin films, due to its large dielectric tunability and low microwave loss at room temperature. BST thin film varactor technology based reconfigurable radio frequency (RF)/microwave components have been demonstrated with the potential to lower the size, weight, and power needs of a future generation of communication and radar systems. Low-power multiferroic devices have also been recently demonstrated. Strong magneto-electric coupling has also been demonstrated in different multiferroic heterostructures, which show giant voltage control of the ferromagnetic resonance frequency of more than two octaves. This manuscript reviews recent advances in the processing, and application development for the complex oxides and multiferroics, with the focus on voltage tunable RF/microwave components. The over-arching goal of this review is to provide a synopsis of the current state-of the-art of complex oxide and multiferroic thin film materials and devices, identify technical issues and technical challenges that need to be overcome for successful insertion of the technology for both military and commercial applications, and provide mitigation strategies to address these technical challenges.
Hysteretic ac loss of a superconductor strip subject to an oscillating transverse magnetic field: Geometrical and electromagnetic effects
Authors: Rauh H. , Ma G. T.
Published: November 2013

Numerical simulations of geometrical and electromagnetic effects on the distributions of the magnetic induction, the electric field, the current density, the power loss density, and the hysteretic ac loss of a type-II superconductor strip exposed to an oscillating transverse magnetic field are performed by resorting to the quasistatic approximation of a vector potential approach. The underlying definition of the superconducting constituent makes use of a generalized “smoothed” Bean model of the critical state, which includes the field dependence of the induced current as well. Based on the Jacobian-free Newton-Krylov approach and the backward Euler scheme, the numerical analysis at hand is tailored to the problem of a variable width/thickness aspect ratio of the superconductor strip. Assigning representative materials characteristics and conditions of the applied magnetic field, the main findings include: (i) at high amplitudes of the applied magnetic field, variations of the magnetic induction, the induced electric field, the induced current density, and the power loss density across the thickness of the strip die away as the latter quantity abates; (ii) at low and moderate amplitudes of the applied magnetic field, the hysteretic ac loss abates rapidly, as the aspect ratio of the strip augments, the field dependence of the induced current merely playing an insignificant part thereby; conversely, whereas the geometrical effect controlled by the aspect ratio of the strip is minute at high amplitudes of the applied magnetic field, a reduction of the hysteretic ac loss occurs due to Kim's extended Ansatz for the critical state.
Linear-scaling explicitly correlated treatment of solids: Periodic local MP2-F12 method
Authors: Usvyat Denis
Published: November 2013

Theory and implementation of the periodic local MP2-F12 method in the 3*A fixed-amplitude ansatz is presented. The method is formulated in the direct space, employing local representation for the occupied, virtual, and auxiliary orbitals in the form of Wannier functions (WFs), projected atomic orbitals (PAOs), and atom-centered Gaussian-type orbitals, respectively. Local approximations are introduced, restricting the list of the explicitly correlated pairs, as well as occupied, virtual, and auxiliary spaces in the strong orthogonality projector to the pair-specific domains on the basis of spatial proximity of respective orbitals. The 4-index two-electron integrals appearing in the formalism are approximated via the direct-space density fitting technique. In this procedure, the fitting orbital spaces are also restricted to local fit-domains surrounding the fitted densities. The formulation of the method and its implementation exploits the translational symmetry and the site-group symmetries of the WFs. Test calculations are performed on LiH crystal. The results show that the periodic LMP2-F12 method substantially accelerates basis set convergence of the total correlation energy, and even more so the correlation energy differences. The resulting energies are quite insensitive to the resolution-of-the-identity domain sizes and the quality of the auxiliary basis sets. The convergence with the orbital domain size is somewhat slower, but still acceptable. Moreover, inclusion of slightly more diffuse functions, than those usually used in the periodic calculations, improves the convergence of the LMP2-F12 correlation energy with respect to both the size of the PAO-domains and the quality of the orbital basis set. At the same time, the essentially diffuse atomic orbitals from standard molecular basis sets, commonly utilized in molecular MP2-F12 calculations, but problematic in the periodic context, are not necessary for LMP2-F12 treatment of crystals.
Effect of the substrate orientation on the formation of He-plates in Si
Authors: Vallet M. , Barbot J. F. , Declémy A. , Reboh S. , Beaufort M. F.
Published: November 2013

The effect of the crystalline orientation on the implantation-induced strain/stress and on the formation of He-plates was studied by combining high-resolution X-ray scattering and transmission electron microscopy. The highest strains are obtained in (001)-oriented implanted substrates regardless of the fluence and of the channeling effects. The anisotropic properties of the silicon that generate an anisotropic elastic response of the substrate were taken into account to explain these different values of strain. Upon specific thermal annealing, it is shown that the formation of He-plates occurs only in the {001} habit planes regardless of the orientation of the substrates, non-tilted and tilted (001)-, (110)-, and (111)-substrates. Moreover, the distribution of He-plates in the {001} variants was found to be strongly dependent on the angle of the habit plane with the surface and on the intensity of the implantation-induced strain/stress. The implantation-induced stress thus favors the formation of He-plates in specific planes (of low angle with the surface) forming different defect configurations. The nucleation and growth of He-plates are thus discussed with regard to the implantation-induced stress.
Assignments of the Raman modes of monoclinic erbium oxide
Authors: Yan D. , Wu P. , Zhang S. P. , Liang L. , Yang F. , Pei Y. L. , Chen S.
Published: November 2013

As a heavy rare earth oxide, erbium oxide (Er2O3) has many attractive properties. Monoclinic Er2O3 has useful properties not found in stable cubic Er2O3, such as unique optical properties and high radiation damage tolerance. In this study, cubic Er2O3 coating and Er2O3 coating with mixed phases were prepared. The Raman scattering spectra of these coatings were investigated by using a confocal micro-Raman spectrometer equipped with 325, 473, 514, 532, 633, and 784 nm lasers. A total of 17 first-order Raman modes of monoclinic Er2O3 were identified and assigned. The modes at 83, 112, 152, 170, 278, 290, 409, 446, 478, 521, 603, and 622 cm−1 are of Ag symmetry, whereas modes at 71, 98, 333, 409, 446, and 468 cm−1 are of Bg symmetry. This research provides basic data necessary for the characterization of monoclinic Er2O3 by Raman spectroscopy.
Effects of electric field and shape on the ground state energy of an exciton bound to an ionized donor impurity in ellipsoidal quantum dots
Authors: Shi Lei , Yan Zuwei
Published: November 2013

The effects of electric field and shape on the ground state energy of an exciton bound to an ionized donor are studied in a weakly prolate (oblate) GaAs ellipsoidal quantum dot within the effective-mass approximation using a variational method in the framework of perturbation theory. Both the heavy-hole and light-hole excitons are considered. The results show that the energy shift not only depends on the electric field but also on the dot shape and size. The influence of the dot shape on the light hole case is more pronounced than that of the heavy hole case, but the influence of the electric field on the heavy hole case is more pronounced.
Effect of magnetic field on binodal temperature in immiscible alloys
Authors: Bian Xiufang , Zhao Xiaolin , Wu Yuqin , Guo Kai
Published: November 2013

The variation of the binodal temperatures for the different immiscible alloys, CdGa and BiGa, was determined through the dynamic viscosity measurements of melts under various external magnetic field conditions. The binodal temperature change was controlled by an energy barrier during solidification. An energy barrier equation is proposed to quantitatively calculate the activation energy during liquid phase separation process for the immiscible alloys. The relationship between the energy barrier and the magnetic field intensity has been established. The magnetic field not only causes an increase of melt viscosity for the immiscible alloys but also makes the melts becoming much stronger. The binodal temperature of the immiscible alloy obviously shifts to higher temperature as the magnetic field intensity increases. An anomaly that the viscosity of immiscible alloys decreases with decreasing temperature is uncovered.
Monolithic ultrasonic integrated circuits based on micromachined semi-ellipsoidal piezoelectric domes
Authors: Hajati Arman , Latev Dimitre , Gardner Deane , Ottosson Mats , Imai Darren , Torrey Marc , Schoeppler Martin
Published: November 2013

We have developed high performance acoustic chips containing arrays of three-dimensional micromachined semi-ellipsoidal piezoelectric domes. The eigenfrequencies and mode shapes of the semi-ellipsoidal resonators are determined by the semi-principal axis lengths and also the acoustic loading by other resonators. By overlapping several modes of vibration, while considering the complex acoustic interaction between elements, highly efficient operation and an ultra wide-bandwidth frequency (up to 165%) response have been achieved from devices comprising multiple resonators. Customizable performance capabilities and high sensitivity (up to 300 W/cm2) at low-operating voltage (10 V amplitude) suitable for both therapeutic and imaging applications are demonstrated.
Correlation between thermal annealing temperature and Joule-heating based insulator-metal transition in VO2 nanobeams
Authors: Rathi Servin , Park Jin-Hyung , Lee In-yeal , Jin Kim Min , Min Baik Jeong , Kim Gil-Ho
Published: November 2013

Rapid thermal annealing of VO2 nanobeams in an ambient argon environment has been carried out at various temperatures after device fabrication. Our analysis revealed that increasing the annealing temperature from 200 °C to 400 °C results in the reduction of both ohmic and nanobeam resistances with an appreciable decrease in joule-heating based transition voltage and transition temperature, while samples annealed at 500 °C exhibited a conducting rutile-phase like characteristics at room temperature. In addition, these variation trends were explored using a physical model and the results were found to be in agreement with the observed results, thus verifying the model.
Is phytotoxicity of Phragmites australis residue influenced by decomposition condition, time and density?
Authors: Uddin Md. N. , Robinson Randall W. , Caridi Domenic , Harun Md. A. Y.
Published: November 2013

Phragmites australis is an invasive wetland plant and allelopathy appears to contribute to its invasiveness. We studied dynamics of physicochemical characteristics and phytotoxicity through residue decomposition of Phragmites with and without soil under different conditions and density over time. Physicochemical variables (water-soluble phenolics, dissolved organic carbon, specific ultraviolet absorbance, pH, electrical conductivity, osmotic potential and some anions, namely PO43–, Cl–, NO2–, NO3– and SO42–) of extracts were more consistent and showed normal range in aerobic rather than anaerobic conditions. ‘Residue alone’ and ‘residue with soil’ extracts exhibited significant inhibition on germination and growth of Poa labillardierei and Lactuca sativa initially but reduced over time in aerobic conditions whereas the inhibition increased sharply and remained almost stable in anaerobic conditions (P ≤ 0.001). Regression analyses showed that water-soluble phenolics were a significant predictor of the inhibitory effects on germination and growth of tested species compared with other variables in the extracts. Long-term decomposed residues exhibited significant effects on germination and growth of Melaleuca ericifolia (P ≤ 0.01) depending on residue density in soil. The results demonstrated that decomposition condition and soil incorporation coupled with residue density may play a crucial role over time in dynamics of physicochemical variables and associated phytotoxicity. The study contributes to understanding of the ecological consequences of phytotoxins in residue decomposition, partially explaining the invasion process of Phragmites in wetlands and thereby improving wetland management.
Regularity in the growth of the loop space homology of a finite CW complex
Authors: Félix Yves , Halperin Steve , Thomas Jean-Claude
Published: November 2013

To any path connected topological space

X
X

, such that

rk
⁡

H
i

(
X
)
>
∞

\operatorname {rk} H_i(X) >\infty

for all

i
≥
0

i\geq 0

, are associated the following two sequences of integers:

b
i

=
rk
⁡

H
i

(
Ω
X
)

b_i= \operatorname {rk} H_i(\Omega X)

and

r
i

=
rk
⁡

π

i
+
1

(
X
)

r_i= \operatorname {rk} \pi _{i+1}(X)

. If

X
X

is simply connected, the Milnor-Moore theorem together with the Poincaré-Birkoff-Witt theorem provides an explicit relation between these two sequences. If we assume moreover that

H
i

(
X
;

Q

)
=
0

H_i(X;\mathbb Q)=0

, for all

i
≫
0

i\gg 0

, it is a classical result that the sequence of Betti numbers

(

b
i

)

(b_i)

grows polynomially or exponentially, depending on whether the sequence

(

r
i

)

(r_i)

is eventually zero or not. The purpose of this note is to prove, in both cases, that the

r

t
h

r^{\mathrm {th}}

Betti number

b
r

b_r

is controlled by the immediately preceding ones. The proof of this result is based on a careful analysis of the Sullivan model of the free loop space

X

S
1

X^{S^1}

.
ISCB: past–present perspective for the International Society for Computational Biology
Authors: Rost Burkhard
Published: November 2013

Since its establishment in 1997, International Society for Computational Biology (ISCB) has contributed importantly toward advancing the understanding of living systems through computation. The ISCB represents nearly 3000 members working in >70 countries. It has doubled the number of members since 2007. At the same time, the number of meetings organized by the ISCB has increased from two in 2007 to eight in 2013, and the society has cemented many lasting alliances with regional societies and specialist groups. ISCB is ready to grow into a challenging and promising future. The progress over the past 7 years has resulted from the vision, and possibly more importantly, the passion and hard working dedication of many individuals.
footprintDB: a database of transcription factors with annotated cis elements and binding interfaces
Authors: Sebastian Alvaro , Contreras-Moreira Bruno
Published: November 2013

Motivation: Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases.

Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value.

Availability and implementation: Web site implemented in PHP, Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

Contact: bioquimicas@yahoo.es; bcontreras@eead.csic.es

Supplementary information: Supplementary data are available at Bioinformatics online.
Primary Care Guidelines for the Management of Persons Infected With HIV: 2013 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Aberg Judith A. , Gallant Joel E. , Ghanem Khalil G. , Emmanuel Patricia , Zingman Barry S. , Horberg Michael A.
Published: November 2013

Evidence-based guidelines for the management of persons infected with human immunodeficiency virus (HIV) were prepared by an expert panel of the HIV Medicine Association of the Infectious Diseases Society of America. These updated guidelines replace those published in 2009. The guidelines are intended for use by healthcare providers who care for HIV-infected patients. Since 2009, new antiretroviral drugs and classes have become available, and the prognosis of persons with HIV infection continues to improve. However, with fewer complications and increased survival, HIV-infected persons are increasingly developing common health problems that also affect the general population. Some of these conditions may be related to HIV infection itself or its treatment. HIV-infected persons should be managed and monitored for all relevant age- and sex-specific health problems. New information based on publications from the period 2009–2013 has been incorporated into this document.
Novel functional APOB mutations outside LDL-binding region causing familial hypercholesterolaemia
Authors: Alves Ana Catarina , Etxebarria Aitor , Soutar Anne Katherine , Martin Cesar , Bourbon Mafalda
Published: November 2013

Familial hypercholesterolaemia (FH) is characterized by increased circulating low-density lipoprotein (LDL) cholesterol leading to premature atherosclerosis and coronary heart disease. Although FH is usually caused by mutations in LDLR, mutations in APOB and PCSK9 also cause FH but only a few mutations have been reported, APOB p.R3527Q being the most common. However, 30–80% of clinical FH patients do not present an identifiable mutation in any of the described genes. To identify the genetic cause of the hypercholesterolaemia in 65 patients without mutations in LDLR, PCSK9 or in fragments of exon 26 and 29 of APOB currently analysed, we performed whole sequencing of APOB by pyrosequencing. A total of 10 putative mutations in APOB were identified. Flow cytometry with fluorescently labelled LDL from patients and relatives showed that p.Arg1164Thr (exon 22) and p.Gln4494del (exon 29) presented a 40% decrease in internalization in lymphocytes and HepG2 cells, very similar to APOB3527. The proliferation assays with U937 cells showed reduced growth for both cases. The variant p.Tyr1247Cys was found to be neutral and other three alterations were considered polymorphisms. Our results emphasize the need to study the whole APOB in routine protocols to improve patient identification and cardiovascular risk assessment.
Genetic marking of farmed Atlantic cod (Gadus morhua l.) and detection of escapes from a commercial cod farm
Authors: Jørstad Knut E. , Otterå Håkon , van der Meeren Terje , Dahle Geir , Paulsen Ole I. , Bakke Gunnar , Svåsand Terje
Published: November 2013

A genetically marked Atlantic cod (Gadus morhua L.) strain was used to identify escapes from commercial cod farms, and to investigate the potential interbreeding between farmed and wild cod. This farmed cod was homozygote for a rare allele (30) in the GPI-1 locus expressed in white muscle tissue. Juveniles were produced from this strain in 2007 and 2008, and 500 000 individuals of each year class were transported to a cod farm in western Norway, where they were raised under commercial conditions. A monitoring fishing program was established from spring 2007 to detect escapees during the farming period. The first farmed cod escapees, identified to the 2007 year class through the genetic mark, age and body size, were detected during the fishing survey in November 2008. The second escape of the same year class was detected during the natural spawning season in early April 2009. A third escape was detected in November 2009, and this time the farmed cod were identified to the 2008 year class. The escapees were spreading through the whole fjord system, including local spawning sites for wild cod. Detailed examination of the escaped cod revealed a substantial degree of sexual maturation, and nearly 1000 cod larvae and early juveniles were therefore collected through spring 2009. The genetic analyses identified eight of these as genetically marked, demonstrating successful reproduction either in the cage or after escape. Interbreeding between escaped and wild cod may also have occurred, but cannot be proven from our material. In all years after the three identified escapes, genetically marked cod were found in the fjord area. In addition, several specimens were observed in adjacent fjord systems, demonstrating long-term survival in the local spawning areas as well as substantial spread over larger distances.