bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local administration of alendronate reduced peri‐tunnel bone loss and promoted graft‐bone tunnel healing with minimal systemic effect on bone in contralateral knee
Authors: Lui Pauline Po Yee , Lee Yuk Wa , Mok Tsui Yu , Cheuk Yau Chuk 
Published: July 2013

ABSTRACTContinued systemic administration of alendronate was reported to reduce peri‐tunnel bone resorption and promoted graft‐bone tunnel healing at the early stage post‐anterior cruciate ligament (ACL) reconstruction. However, systemic increase in bone mineral density (BMD) in the contralateral intact knee was observed. We tested if single local administration of alendronate into the bone tunnel during ACL reconstruction could achieve similar benefits yet without the systemic effect on bone. Seventy‐two rats with unilateral ACL reconstruction were divided into three groups: saline, low‐dose (6 μg/kg) and mid‐dose (60 μg/kg) alendronate. For local administration, alendronate was applied to the bone tunnels for 2 min before graft insertion and repair. At weeks 2 and 6, the reconstructed complex was harvested for high‐resolution computed tomography (vivaCT) imaging followed by biomechanical test or histology. Our results showed that local administration of low‐dose alendronate showed comparable benefits on the reduction of peri‐tunnel bone loss, enhancement of bone tunnel mineralization, tunnel graft integrity, graft osteointegration and mechanical strength of the reconstructed complex at early stage post‐reconstruction, yet with minimal systemic effect on mineralized tissue at the contralateral intact knee. A single local administration of alendronate at the low‐dose therefore might be used to promote early tunnel graft healing post‐reconstruction. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:1897–1906, 2013
Continuous‐wave vertically emitting photonic crystal terahertz laser
Authors: Diao Zhaolu , Bonzon Christopher , Scalari Giacomo , Beck Mattias , Faist Jérôme , Houdré Romuald 
Published: July 2013

AbstractCompact semiconductor light sources with high performance continuous‐wave (CW) and single mode operation are highly demanded for many applications in the terahertz (THz) frequency range. Distributed feedback (DFB) and photonic crystal (PhC) quantum cascade (QC) lasers are amongst the leading candidates in this field. Absorbing boundary condition is a commonly used method to control the optical performance of a laser in double‐metal confinement. However, this approach increases the total loss in the device and results in a large threshold current density, limiting the CW maximum output power and operating temperature. In this letter, a robust surface emitting continuous‐wave terahertz QC laser is realized in a two‐dimensional PhC structure by a second order Bragg grating extractor that simultaneously provides the boundary condition necessary for mode selection. This results in a 3.12 THz single mode CW operation with a 3 mW output power and a maximum operation temperature (Tmax) of 100 K. Also, a highly collimated far‐field pattern is demonstrated, which is an important step towards real world applications.
Self‐phase‐locked degenerate femtosecond optical parametric oscillator based on BiB3O6
Authors: Ramaiah‐Badarla Venkata , Esteban‐Martin Adolfo , Ebrahim‐Zadeh Majid 
Published: July 2013

AbstractA self‐phase‐locked degenerate femtosecond optical parametric oscillator (OPO) based on the birefringent nonlinear material, bismuth triborate, BiB3O6, synchronously‐pumped by a Kerr‐lens‐mode‐locked Ti:sapphire laser at 800 nm is described. By exploiting versatile phase‐matching properties of BiB3O6, including large spectral and angular acceptance for parametric generation and low group velocity dispersion in the optical xz plane, stable self‐phase‐locked degenerate OPO operation centered at 1600 nm is demonstrated using collinear type I (e → oo) interaction in a 1.5‐mm crystal at room temperature.The degenerate OPO output spectrum extends over 46 nm (∼5.4 THz) with 190 fs pulse duration for input pump pulses of 155 fs with a bandwidth of 7 nm. Phase coherence between the pump and degenerate output is verified using f‐2f interferometry, and discrete frequency beats caused by different carrier‐envelope‐offset frequencies are measured using radio frequency measurements.Photo shows a 1.5‐mm BiB3O6 crystal used as a nonlinear gain medium in a degenerate self‐phase‐locked femtosecond OPO operating at room temperature. The green beam is the result of non‐phase‐matched sum‐frequency mixing between the pump light and the sub‐harmonic OPO field at degeneracy.
Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand
Authors: Mohan Vathsala , Stevenson Mark , Marshall Jonathan , Fearnhead Paul , Holland Barbara R. , Hotter Grant , French Nigel P. 
Published: July 2013

AbstractA repeated cross‐sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by FST, and host‐genotype association with clonal complexes CC ST‐177 and CC ST‐682 associated with starlings, and clonal complexes CC ST‐1034, CC ST‐692, and CC ST‐1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host‐associated genotypes, such as the starling‐associated ST‐177 and ST‐682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas.
Identification of a metagenomic gene cluster containing a new class A beta‐lactamase and toxin‐antitoxin systems
Authors: Vercammen Ken , Garcia‐Armisen Tamara , Goeders Nathalie , Van Melderen Laurence , Bodilis Josselin , Cornelis Pierre 
Published: July 2013

AbstractSeveral reports mention the presence of antibiotic resistance genes in natural and polluted environments, but many studies are based on their detection via polymerase chain reaction (PCR amplification of known genes and not on an activity screening. We constructed a metagenomic fosmid bank from DNA isolated from a polluted river in Brussels, Belgium, the Zenne. A total of 120,000 clones were pooled and plated directly on solid media containing different antibiotics. Several clones were isolated which could grow in the presence of ampicillin. The DNA from several clones was extracted and subjected to restriction analysis and, based on their restriction pattern, two different clones were found. One of the clones was selected for further study as it showed a higher level of resistance to different β‐lactams antibiotics (ticarcilline and ceftazidime). To find out which gene is responsible for the resistance, an in vitro transposon mutagenesis was performed and clones having lost the resistance phenotype were analyzed via inverse PCR amplification. Several clones had an insert in a gene encoding a new type of β‐lactamase. The amplified fosmid DNA was fully sequenced revealing an insert of 41 kb containing 39 open reading frames (ORFs). Transposon insertions inactivating the resistance to β‐lactams were also found in the ORF upstream of the blaA gene, encoding an aminotransferase, suggesting a polar effect on the transcription of the gene downstream. In addition, other genes were found such as histidine biosynthesis genes, which were found to be scattered on the insert, a relA/spoT gene, and genes belonging to type II toxin–antitoxin system. This predicted system was experimentally validated in Escherichia coli using an inducible expression system.
Identification in Marinomonas mediterranea of a novel quinoprotein with glycine oxidase activity
Authors: Campillo‐Brocal Jonatan Cristian , Lucas‐Elio Patricia , Sanchez‐Amat Antonio 
Published: July 2013

AbstractA novel enzyme with lysine‐epsilon oxidase activity was previously described in the marine bacterium Marinomonas mediterranea. This enzyme differs from other l‐amino acid oxidases in not being a flavoprotein but containing a quinone cofactor. It is encoded by an operon with two genes lodA and lodB. The first one codes for the oxidase, while the second one encodes a protein required for the expression of the former. Genome sequencing of M. mediterranea has revealed that it contains two additional operons encoding proteins with sequence similarity to LodA. In this study, it is shown that the product of one of such genes, Marme_1655, encodes a protein with glycine oxidase activity. This activity shows important differences in terms of substrate range and sensitivity to inhibitors to other glycine oxidases previously described which are flavoproteins synthesized by Bacillus. The results presented in this study indicate that the products of the genes with different degrees of similarity to lodA detected in bacterial genomes could constitute a reservoir of different oxidases.
Transcriptomic and phenotypic analysis of paralogous spx gene function in Bacillus anthracis Sterne
Authors: Barendt Skye , Lee Hyunwoo , Birch Cierra , Nakano Michiko M. , Jones Marcus , Zuber Peter 
Published: July 2013

AbstractSpx of Bacillus subtilis is a redox‐sensitive protein, which, under disulfide stress, interacts with RNA polymerase to activate genes required for maintaining thiol homeostasis. Spx orthologs are highly conserved among low %GC Gram‐positive bacteria, and often exist in multiple paralogous forms. In this study, we used B. anthracis Sterne, which harbors two paralogous spx genes, spxA1 and spxA2, to examine the phenotypes of spx null mutations and to identify the genes regulated by each Spx paralog. Cells devoid of spxA1 were sensitive to diamide and hydrogen peroxide, while the spxA1 spoxA2 double mutant was hypersensitive to the thiol‐specific oxidant, diamide. Bacillus anthracis Sterne strains expressing spxA1DD or spxA2DD alleles encoding protease‐resistant products were used in microarray and quantitative real‐time polymerase chain reaction (RT‐qPCR) analyses in order to uncover genes under SpxA1, SpxA2, or SpxA1/SpxA2 control. Comparison of transcriptomes identified many genes that were upregulated when either SpxA1DD or SpxA2DD was produced, but several genes were uncovered whose transcript levels increased in only one of the two SpxADD‐expression strains, suggesting that each Spx paralog governs a unique regulon. Among genes that were upregulated were those encoding orthologs of proteins that are specifically involved in maintaining intracellular thiol homeostasis or alleviating oxidative stress. Some of these genes have important roles in B. anthracis pathogenesis, and a large number of upregulated hypothetical genes have no homology outside of the B. cereus/thuringiensis group. Microarray and RT‐qPCR analyses also unveiled a regulatory link that exists between the two spx paralogous genes. The data indicate that spxA1 and spxA2 are transcriptional regulators involved in relieving disulfide stress but also control a set of genes whose products function in other cellular processes.
Validation of quantitative bound‐ and pore‐water imaging in cortical bone
Authors: Manhard Mary Kate , Horch R. Adam , Harkins Kevin D. , Gochberg Daniel F. , Nyman Jeffry S. , Does Mark D. 
Published: July 2013

PurposeTo implement and validate a previously proposed ultra‐short echo time method for measuring collagen‐bound‐ and pore‐water concentrations in bone based on their T2 differences.MethodsClinically compatible ultra‐short echo time image sequences for quantitative T2‐based bound and pore‐water imaging in bone were implemented and validated on a 3T human scanner and a 4.7T small bore system. Bound‐ and pore‐water images were generating using T2‐selective adiabatic pulses. In both cases, the magnetization preparation was integrated into a three‐dimensional ultra‐short echo time acquisition, with 16 radial spokes acquired per preparation. Images were acquired from human cadaveric femoral mid‐shafts from which isolated bone samples were subsequently extracted for nonimaging analysis using T2 spectroscopic measurements.ResultsA strong correlation was found between imaging‐derived concentrations of bound and pore water and those determined from the isolated bone samples.ConclusionsThese studies demonstrate the translation of the previously developed approaches for distinguishing bound and pore water from human cortical bone using practical human MRI constraints of gradient performance and radiofrequency power deposition. Magn Reson Med 71:2166–2171, 2014. © 2013 Wiley Periodicals, Inc.
Three‐dimensional Fourier encoding of simultaneously excited slices: Generalized acquisition and reconstruction framework
Authors: Zahneisen Benjamin , Poser Benedikt A. , Ernst Thomas , Stenger V. Andrew 
Published: July 2013

PurposeSimultaneous multislice (SMS) acquisitions have recently received much attention as a means of increasing single‐shot imaging speed. SMS acquisitions combine the advantages of single‐shot sampling and acceleration along the slice dimension which was previously limited to three‐dimensional (3D) volumetric acquisitions. A two‐dimensional description of SMS sampling and reconstruction has become established in the literature. Here, we present a more general 3D Fourier encoding and reconstruction formalism for SMS acquisitions that can easily be applied to non‐Cartesian SMS acquisitions.Theory and MethodsAn “SMS 3D” k‐space is defined in which the field of view along the slice select direction is equal to the number of excited slices times their separation. In this picture, SMS acceleration can be viewed as an undersampling of SMS 3D k‐space that can be freely distributed between the in‐plane and slice directions as both are effective phase‐encoding directions.ResultsUse of the SMS 3D k‐space picture is demonstrated in phantom and in vivo brain acquisitions including data obtained with blipped‐controlled aliasing in parallel imaging sampling. SMS sensitivity encoding reconstruction is demonstrated as well as non‐Cartesian SMS imaging using blipped spiral trajectories.ConclusionsThe full framework of reconstruction methods can be applied to SMS acquisitions by employing a 3D k‐space approach. The blipped‐controlled aliasing in parallel imaging method can be viewed as a special case of undersampling an SMS 3D k‐space. The extension of SMS methods to non‐Cartesian 3D sampling and reconstruction is straightforward. Magn Reson Med 71:2071–2081, 2014. © 2013 Wiley Periodicals, Inc.
RAZER: A pulse sequence for whole‐brain bolus tracking at high frame rates
Authors: Jonathan Sumeeth V. , Vakil Parmede , Jeong Yong I. , Menon Rajiv G. , Ansari Sameer A. , Carroll Timothy J. 
Published: July 2013

PurposeTo introduce a pulse sequence that obtains whole‐brain perfusion measurements at 1.7 mm isotropic voxel resolution by dynamic susceptibility contrast MRI bolus tracking despite using a temporal resolution of 10.3 s: RAdial kZ‐blipped 3D GRE‐echo‐planar imaging (GRE‐EPI) for whole‐brain pERfusion (RAZER).MethodsIn RAZER, in‐plane radial and through‐plane 3D GRE‐EPI Cartesian sampling was used to produce a 3D stack‐of‐stars k‐space. In vivo scans on one healthy volunteer and one patient with Moyamoya disease were performed using RAZER and a typical 2D GRE‐EPI pulse sequence as a reference standard. Agreement in perfusion metrics was reported using linear regression analysis and Bland‐Altman plots.ResultsSliding window reconstruction recovered dynamic information lost in the large temporal acquisition window of RAZER. Inline phase correction scans corrected N/2 ghosting artifacts and view‐dependent phase variations. Whole‐brain images of cerebral blood volume, cerebral blood flow, and mean transit time were calculated with RAZER at 1.7 mm isotropic voxel resolution and good reference standard agreement in both subjects when sliding window reconstruction was used (r2 > 0.7, mean bias in mean transit time measurements < 0.5 s).ConclusionsDespite using a temporal resolution of 10.3 s, in vivo data indicates that RAZER is able to obtain whole‐brain perfusion measurements at 1.7 mm isotropic voxel resolution and good reference standard agreement. Magn Reson Med 71:2127–2138, 2014. © 2013 Wiley Periodicals, Inc.
Variational sensitivity analysis of a nonlinear solid shell element
Authors: Gerzen N. , Barthold F. J. , Klinkel S. , Wagner W. , Materna D. 
Published: July 2013

SUMMARYThe paper is concerned with variational sensitivity analysis of a nonlinear solid shell element, which is based on the Hu–Washizu variational principle. The sensitivity information is derived on the continuous level and discretized to yield the analytical expressions on the computational level. Especially, the pseudo load matrix and the sensitivity matrix, which dominate design sensitivity analysis of shape optimization problems, are derived. Because of the mixed formulation, condensation of the pseudo load matrix on the element level is performed to compute the sensitivity matrix. An illustrative example from the field of geometry‐based shape optimization demonstrates the possible application of the presented formulation. Copyright © 2013 John Wiley & Sons, Ltd.
Is graphene on copper doped?
Authors: Marsden Alexander J. , Asensio Maria‐Carmen , Avila José , Dudin Pavel , Barinov Alexei , Moras Paolo , Sheverdyaeva Polina M. , White Thomas W. , Maskery Ian , Costantini Giovanni , Wilson Neil R. , Bell Gavin R. 
Published: July 2013

AbstractAngle‐resolved photoemission spectroscopy (ARPES) and X‐ray photoemission spectroscopy have been used to characterise epitaxially ordered graphene grown on copper foil by low‐pressure chemical vapour deposition. A short vacuum anneal to 200 °C allows observation of ordered low energy electron diffraction patterns. High quality Dirac cones are measured in ARPES with the Dirac point at the Fermi level (undoped graphene). Annealing above 300 °C produces n‐type doping in the graphene with up to 350 meV shift in Fermi level, and opens a band gap of around 100 meV.magnified imageDirac cone dispersion for graphene on Cu foil after vacuum anneals (left: 200 °C, undoped; right: 500 °C, n‐doped). Centre: low energy electron diffraction from graphene on Cu foil after 200 °C anneal. Data from Antares (SOLEIL).(© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Equivalent circuit model of a nanogenerator based on a piezoelectric nanowire–polymer composite
Authors: Graton Olivier , Poulin‐Vittrant Guylaine , Dahiya Abhishek Singh , Camara Nicolas , Hue Louis‐Pascal Tran Huu , Lethiecq Marc 
Published: July 2013

Abstractmagnified imageA vertically integrated nanogenerator (VING) refers to the new generation of mechanical energy harvesting devices: arrays of piezoelectric and semiconducting nanowires are grown perpendicularly to a substrate and appropriate electrodes enable charge circulation through an external electrical load. In this Letter, an equivalent circuit of VING is proposed. This model takes into account the effect of the polymer matrix that surrounds the nanowire lattice on the electromechanical behaviour of the generator. The active part of the material is then seen as a 1–3 piezocomposite. Simulations were made to study the VING performance in a context of body movement energy harvesting. In particular, it is shown that the strain amplitude and the strain rate of the piezocomposite have an impact on nanogenerator output voltage and output current, respectively. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Immunity and immune response, pathology and pathologic changes: progress and challenges in the immunopathology of yellow fever
Authors: Quaresma Juarez A. S. , Pagliari Carla , Medeiros Daniele B. A. , Duarte Maria I. S. , Vasconcelos Pedro F. C. 
Published: July 2013

SUMMARYYellow fever is a viral hemorrhagic fever, which affects people living in Africa and South America and is caused by the yellow fever virus, the prototype species in the Flavivirus genus (Flaviviridae family). Yellow fever virus infection can produce a wide spectrum of symptoms, ranging from asymptomatic infection or oligosymptomatic illness to severe disease with a high fatality rate. In this review, we focus in the mechanisms associated with the physiopathology of yellow fever in humans and animal models. It has been demonstrated that several factors play a role in the pathological outcome of the severe form of the disease including direct viral cytopathic effect, necrosis and apoptosis of hepatocyte cells in the midzone, and a minimal inflammatory response as well as low‐flow hypoxia and cytokine overproduction. New information has filled several gaps in the understanding of yellow fever pathogenesis and helped comprehend the course of illness. Finally, we discuss prospects for an immune therapy in the light of new immunologic, viral, and pathologic tools. Copyright © 2013 John Wiley & Sons, Ltd.
Variability of areal surface topography parameters due to the change in surface orientation to measurement direction
Authors: Dzierwa Andrzej , Reizer Rafal , Pawlus Pawel , Grabon Wieslaw 
Published: July 2013

SummarySeveral random surface topographies were analyzed. They were measured by optical (Talysurf CCI Lite) method. They represent one‐ and two‐process anisotropic and isotropic surfaces. These surfaces were rotated of ±1° and ±2° by two methods: on the plane table (before measurement) and virtually (after measurement) using the software TalyMap Gold. After each measurement or surface rotation, each surface was levelled. Then, the forms were removed using polynomial of the 3rd degree. Areal surface topography parameters from standard ISO 25178 were calculated. The relative deviations of parameters were determined. The tendency of surface topography changes characteristic to various surface types were analyzed. It was found that change in orientation to the measurement direction of both isotropic and anisotropic surfaces could be substantial source of the measurement uncertainty. Functional parameter Smr and also feature parameters Sda, Sha, Sdv, Shv, and Spd are the mostly sensitive on measurement orientation. Statistical amplitude parameters Sa and Sq are more stable than parameters describing maximum surface height, like Sz, Sp, and Sv. The effect of surface orientation to measurement direction on values of functional parameters from V group was small. It was shown that changes of Sdq, Sdr, and Spc parameters describing hybrid properties due to surface rotation before measurement were smaller than those caused by change in surface orientation after measurement. SCANNING 36:170–183, 2014. © 2013 Wiley Periodicals, Inc.