bluuebunny/crossref_metadata_2025 huggingface dataset:
When gender matters: new insights into the relationships between social systems and the genetic structure of human populations
Authors: Destro Bisol Giovanni , Capocasa Marco , Anagnostou Paolo
Published: October 2012

Due to its important effects on the ecological dynamics and the genetic structure of species, biologists have long been interested in gender‐biased dispersal, a condition where one gender is more prone to move from the natal site. More recently, this topic has attracted a great attention from human evolutionary geneticists. Considering the close relations between residential rules and social structure, gender‐biased dispersal is, in fact, regarded as an important case study concerning the effects of socio‐cultural factors on human genetic variation. It all started with the seminal paper by Mark Seielstad, Erich Minch and Luigi Luca Cavalli Sforza from Stanford University (Seielstad et al. 1998). They observed a larger differentiation for Y‐chromosome than mitochondrial DNA between extant human populations, purportedly a consequence of the prevalence of long‐term patrilocality in human societies. Subsequent studies, however, have highlighted the need to consider geographically close and culturally homogeneous groups, disentangle signals due to different peopling events and obtain unbiased estimates of genetic diversity. In this issue of Molecular Ecology, not only do Marks et al. (2012) adopt an experimental design which addresses these concerns, but they also take a further and important step forward by integrating the genetic analysis of two distant populations, the Basotho and Spanish, with data regarding migration rates and matrimonial distances. Using both empirical evidence and simulations, the authors show that female‐biased migration due to patrilocality might shape the genetic structure of human populations only at short ranges and under substantial differences in migration rates between genders. Providing a quantitative framework for future studies of the effects of residential rules on the human genome, this study paves the way for further developments in the field. On a wider perspective, Marks et al.'s work demonstrates the power of approaches which integrate biological, cultural and demographic lines of evidence in the study of relations between social and genetic structures of human populations.
Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation‐with‐gene‐flow
Authors: Via Sara , Conte Gina , Mason‐Foley Casey , Mills Kelly
Published: October 2012

Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence‐with‐gene‐flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing FST outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between‐population recombination and gene exchange are reduced over large ‘divergence hitchhiking’ (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of FST outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation‐with‐gene‐flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence.
Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
Authors: Wagner Catherine E. , Keller Irene , Wittwer Samuel , Selz Oliver M. , Mwaiko Salome , Greuter Lucie , Sivasundar Arjun , Seehausen Ole
Published: October 2012

Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction‐site‐associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence‐based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher‐level relationships. These patterns have generally been attributed to the very recent origin (<15 000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post‐speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.
The extreme disjunction between Beringia and Europe in Ranunculus glacialis s. l. (Ranunculaceae) does not coincide with the deepest genetic split – a story of the importance of temperate mountain ranges in arctic–alpine phylogeography
Authors: Ronikier M. , Schneeweiss G. M. , Schönswetter P.
Published: October 2012

The arctic–alpine Ranunculus glacialis s. l. is distributed in high‐mountain ranges of temperate Europe and in the North, where it displays an extreme disjunction between the North Atlantic Arctic and Beringia. Based on comprehensive sampling and employing plastid and nuclear marker systems, we (i) test whether the European/Beringian disjunction correlates with the main evolutionary diversification, (ii) reconstruct the phylogeographic history in the Arctic and in temperate mountains and (iii) assess the susceptibility of arctic and mountain populations to climate change. Both data sets revealed several well‐defined lineages, mostly with a coherent geographic distribution. The deepest evolutionary split did not coincide with the European/Beringian disjunction but occurred within the Alps. The Beringian lineage and North Atlantic Arctic populations, which reached their current distribution via rapid postglacial colonization, show connections to two divergent pools of Central European populations. Thus, immigration into the Arctic probably occurred at least twice. The presence of a rare cpDNA lineage related to Beringia in the Carpathians supports the role of these mountains as a stepping stone between temperate Europe and the non‐European Arctic, and as an important area of high‐mountain biodiversity. The temperate and arctic ranges presented contrasting phylogeographic histories: a largely static distribution in the former and rapid latitudinal spread in the latter. The persistence of ancient lineages with a strictly regional distribution suggests that the ability of R. glacialis to survive repeated climatic changes within southern mountain ranges is greater than what recently was predicted for alpine plants from climatic envelope modelling.
Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti
Authors: Zakas Christina , Wares John P.
Published: October 2012

In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high‐population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.
The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps
Authors: Mosca E. , Eckert A. J. , Di Pierro E. A. , Rocchini D. , La Porta Nicola , Belletti P. , Neale D. B.
Published: October 2012

Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay, single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua Mill., Pinus cembra L. and Pinus mugo Turra, across their natural ranges in the Italian Alps and Apennines. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified three to five genetic groups per species. Geographical correlates with these patterns, however, were only apparent for P. cembra. Multivariate environmental variables [i.e. principal components (PCs)] were subsequently tested for association with SNPs using a Bayesian generalized linear mixed model. The majority of the SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated with PC1, corresponding to winter precipitation and seasonal minimum temperature. In A. alba, four SNPs were associated with PC2, corresponding to the seasonal minimum temperature. Functional annotation of those genes with the orthologs in Arabidopsis revealed several genes involved in abiotic stress response. This study provides a detailed assessment of population structure and its association with environment and geography in four coniferous species in the Italian mountains.
Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
Authors: O'Neill Eric M. , Schwartz Rachel , Bullock C. Thomas , Williams Joshua S. , Shaffer H. Bradley , Aguilar‐Miguel X. , Parra‐Olea Gabriela , Weisrock David W.
Published: October 2012

Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome‐wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next‐generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high‐quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome‐wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi‐species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon‐based PTS to rapidly generate large‐scale data for population genetic and phylogenetic‐based research.
Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata
Authors: Chaoui Lamya , Gagnaire Pierre‐Alexandre , Guinand Bruno , Quignard Jean‐Pierre , Tsigenopoulos Costas , Kara M. Hichem , Bonhomme François
Published: October 2012

The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to be determined. Here, we explore the genetic basis of alternate habitat use in western Mediterranean populations of the gilthead sea bream (Sparus aurata). Samples from lagoonal and open‐sea habitats were typed for three candidate gene microsatellite loci, seven anonymous microsatellites and 44 amplified fragment length polymorphism markers to test for genotype–environment associations. While anonymous markers globally indicated high levels of gene flow across geographic locations and habitats, non‐neutral differentiation patterns correlated with habitat type were found at two candidate microsatellite loci located in the promoter region of the growth hormone and prolactin genes. Further analysis of these two genes revealed that a mechanism based on habitat choice alone could not explain the distribution of genotype frequencies at a regional scale, thus implying a role for differential survival between habitats. We also found an association between allele size and habitat type, which, in the light of previous studies, suggests that polymorphisms in the proximal promoter region could influence gene expression by modulating transcription factor binding, thus providing a potential explanatory link between genotype and growth phenotype in nature.
Origins of specificity and cross‐talk in metal ion sensing by Bacillus subtilisFur
Authors: Ma Zhen , Faulkner Melinda J. , Helmann John D.
Published: October 2012

Fur (ferric uptake regulator) is the master regulator of iron homeostasis in many bacteria, but how it responds specifically to Fe(II) in vivo is not clear. Biochemical analyses of Bacillus subtilis Fur (BsFur) reveal that in addition to Fe(II), both Zn(II) and Mn(II) allosterically activate BsFur–DNA binding. Dimeric BsFur co‐purifies with site 1 structural Zn(II) (Fur2Zn2) and can bind four additional Zn(II) or Mn(II) ions per dimer. Metal ion binding at previously described site 3 occurs with highest affinity, but the Fur2Zn2:Me2 form has only a modest increase in DNA binding affinity (approximately sevenfold). Metallation of site 2 (Fur2Zn2:Me4) leads to a ∼ 150‐fold further enhancement in DNA binding affinity. Fe(II) binding studies indicate that BsFur buffers the intracellular Fe(II) concentration at ∼ 1 μM. Both Mn(II) and Zn(II) are normally buffered at levels insufficient for metallation of BsFur site 2, thereby accounting for the lack of cross‐talk observed in vivo. However, in a perR mutant, where the BsFur concentration is elevated, BsFur may now use Mn(II) as a co‐repressor and inappropriately repress iron uptake. Since PerR repression of fur is enhanced by Mn(II), and antagonized by Fe(II), PerR may co‐regulate Fe(II) homeostasis by modulating BsFur levels in response to the Mn(II)/Fe(II) ratio.
High amplitude propagated contractions
Authors: Bharucha A. E.
Published: October 2012

While most colonic motor activity is segmental and non‐propulsive, colonic high amplitude propagated contractions (HAPC) can transfer colonic contents over long distances and often precede defecation. High amplitude propagated contractions occur spontaneously, in response to pharmacological agents or colonic distention. A subset of patients with slow transit constipation have fewer HAPC. In this issue of Neurogastroenterology and Motility, Rodriguez et al. report that anal relaxation during spontaneous and bisacodyl‐induced HAPC exceeds anal relaxation during rectal distention in constipated children undergoing colonic manometry. Moreover, and consistent with a neural mechanism, anal relaxation often precedes arrival of HAPC in the left colon. High amplitude propagated contractions are also used to evaluate the motor response to a meal and pharmacological stimuli (e.g., bisacodyl, neostigmine) and to identify colonic inertia during colonic motility testing in chronic constipation. This editorial comprehensively reviews the characteristics, physiology and pharmacology of HAPC, their assessment by manometry, and relevance to constipation and diarrhea.
A literature review on flow‐rate variability in neonatal IV therapy
Authors: van der Eijk Anne C. , van Rens Roland M.F.P.T. , Dankelman Jenny , Smit Bert J.
Published: October 2012

Aim

To provide an overview of factors influencing the flow rate in intravenous (IV) therapy for newborns.

Methods

We conducted a review of the literature from 1980 to 2011 in PubMed and Web of Knowledge. Articles focusing on flow‐rate variability and possible complications due to flow‐rate variability were included.

Results

Forty‐one articles were selected for this review. IV therapy in (preterm) neonates is prone to significant start‐up delays and flow‐rate variability. The sudden changes in the volume delivered to (preterm) neonates may have serious consequences. Low preprogrammed flow rates, total compliance, and volume of the IV administration set, the presence or absence of antisiphon valves or inline filters and the vertical displacement of syringe pumps all contribute to flow‐rate variability in IV therapy for neonates.

Conclusions

Flow‐rate variability in IV therapy and its clinical relevance are due to the preprogrammed flow rate, the hydrostatic pressure changes, the complete IV administration set compliance and the type of substances supplied to the patient. To improve IV therapy, the internal compliance of the complete IV administration set should be minimized and the highest possible preprogrammed flow rate should be used in combination with small syringes and low‐resistance valves.
Drought stress adaptation: metabolic adjustment and regulation of gene expression
Authors: Bhargava Sujata , Sawant Kshitija
Published: October 2012

Plants cope with drought stress by manipulating key physiological processes like photosynthesis, respiration, water relations, antioxidant and hormonal metabolism. There exist multiple and often redundant stress sensors, which transduce the stress signal through secondary signalling molecules to the nucleus, where the expression of stress‐response genes is regulated. Transcription factors play an important role in regulating the expression of the stress‐response genes. Another level of regulation of gene expression is at the epigenetic level and involves modifications either at the chromatin level or at the mRNA level. Crop plants show various adaptive and acclimatization strategies to drought stress, which range from seemingly simple morphological or physiological traits that serve as important stress tolerance markers to major upheavals in gene expression in which a large number of transcription factors are induced. Studies on contrasting crop genotypes or genetic engineering of crops help in differentiating responses to drought from those leading to drought tolerance. Of specific importance to crop plants is not whether they survive stress, but whether they show good yields under stress conditions.
64, XX, SRY‐negative, Testicular DSD Syndrome in a Lusitano Horse
Authors: Torres A , Silva JF , Bernardes N , Sales Luís J , Lopes da Costa L
Published: October 2012

Contents

Here is reported a disorder of sex development found in the Portuguese Lusitano horse breed. The complex genital phenotype included mammary glands, abdominal testes without epididymis, connected through oviducts to pelvic hypoplastic uterine horns and fused vulvar labia majora from which protruded ventrally a penis‐like structure. This structure was presented in a reversed position, the urethral opening placed dorsally in the glans. However, it was functional both for micturition and erection. The horse exhibited female micturition posture and aggressive male‐like behaviour, including flehmen, mounting, thrusting and flagging of the tail. Plasma testosterone concentrations were below detection limits and the genetic evaluation revealed a 64, XX, SRY‐negative karyotype. Surgery consisted in the removal of abdominal gonads followed by amputation of the penis and repositioning of the urethra. This case of reversion between the chromosomal and gonadal sex, associated with mixed anatomical and behavioural phenotype, illustrates that development of the testes may occur in the absence of the SRY gene and that other genetic and cellular pathways leading to gonad differentiation should be investigated.
Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity
Authors: Middleton Christopher P. , Stein Nils , Keller Beat , Kilian Benjamin , Wicker Thomas
Published: October 2012

A 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide diversity of transposable elements (TEs) for several Triticeae taxa, including Triticum aestivum, Hordeum vulgare, Hordeum spontaneum and Secale cereale together with relatives of the A, B and D genome donors of wheat, Triticum urartu (A), Aegilops speltoides (S) and Aegilops tauschii (D). Additional taxa containing the A genome, Triticum monococcum and its wild relative Triticum boeoticum, were also included. The main focus of the analysis was on the genomic composition of TEs as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome comprised 12–15 TE families. The BARE1 element was the largest contributor to all genomes, contributing more than 10% to the overall genome. We also found that several TE families differ strongly in their abundance between species, indicating that TE families can thrive extremely successfully in one species while going virtually extinct in another. Additionally, the nucleotide diversity of BARE1 populations within individual genomes was measured. Interestingly, the nucleotide diversity in the domesticated barley H. vulgare cv. Barke was found to be twice as high as in its wild progenitor H. spontaneum, suggesting that the domesticated barley gained nucleotide diversity from the addition of different genotypes during the domestication and breeding process. In the rye/wheat lineage, sequence diversity of BARE1 elements was generally higher, suggesting that factors such as geographical distribution and mating systems might play a role in intragenomic TE diversity.
On the limit behavior of metrics in the continuity method for the Kähler–Einstein problem on a toric Fano manifold
Authors: Li Chi
Published: October 2012

This work is a continuation of the author’s previous paper [Greatest lower bounds on the Ricci curvature of toric Fano manifolds, Adv. Math. 226(2011), 4921–4932]. On any toric Fano manifold, we discuss the behavior of the limit metric of a sequence of metrics which are solutions to a continuity family of complex Monge–Ampère equations in the Kähler–Einstein problem. We show that the limit metric satisfies a singular complex Monge–Ampère equation. This gives a conic-type singularity for the limit metric. Information on conic-type singularities can be read off from the geometry of the moment polytope.
The Effect of Ultrapolish on a Transonic Axial Rotor
Authors: Roberts William B. , Thorp Scott A. , Prahst Patricia S. , Strazisar Anthony J.
Published: October 2012

Back-to-back testing was done using NASA fan rotor 67 in the Glenn Research Center W8 Axial Compressor Test Facility. The rotor was baseline tested with a normal industrial root-mean-square (RMS) surface finish of 0.5 μm to 0.6 μm (20 microinches to 24 microinches) at 60, 80, and 100% of design speed. At design speed the tip relative Mach number was 1.38. The blades were then removed from the facility and ultrapolished to a surface finish of 0.125 μm (5 microinch) or less and retested. At 100% speed near the design point, the ultrapolished blades showed approximately 0.3% to 0.5% increase in adiabatic efficiency. The difference was greater near maximum flow. Due to increased relative measurement error at 60 and 80% speed, the performance difference between the normal and ultrapolished blades was indeterminate at these speeds.
Fabrication of 1 Teradot/in.2 CoCrPt bit patterned media and recording performance with a conventional read/write head
Authors: Dobisz Elizabeth A. , Kercher Dan , Grobis Michael , Hellwig Olav , Marinero Ernesto E. , Weller Dieter , Albrecht Thomas R.
Published: October 2012

1 Teradot/in.2 (Td/in.2) CoCrPt alloy bit patterned media (BPM) disks were patterned by direct write e-beam lithography, and the recording performance was measured with a commercial recording head. Recording analysis showed a minimum error rate of 2 × 10−3, which was limited by the fraction of BPM patterning defects Continuous magnetic media disks were coated with a 20 nm thick carbon hard mask film by PECVD followed by a 8.5 nm thick hydrogen silsesquioxane (HSQ) resist by spin coating. A series of 1 Td/in.2 dot patterns were e-beam written in the HSQ, and the patterns were etched into the carbon hard mask by reactive ion etching. The underlying magnetic media was physically etched with 200 eV Ar. The carbon hard mask maximum thickness was limited by erosion of the HSQ dots during the carbon hardmask etch and shadowing of the mask during the magnetic media etch. The minimum carbon thickness and the maximum CoCrPt thickness were determined by erosion of the hardmask pillars during etching of the CoCrPt magnetic media. The optimal carbon hard mask thickness was determined to be ∼20 nm (for our PECVD carbon). The optimal CoCrPt magnetic media thickness was 6 nm, as determined by etch selectivity and magnetic properties. A Silvaco Monte Carlo 3D model simulation was used to describe the magnetic media etching process. Additional patterning steps formed physical support, surrounding the patterns, for the recording head that scanned in contact with the patterned magnetic media. Analysis of top down SEM micrographs of BPM patterns showed defect rates as low as 3 × 10−4 and a 1-sigma dot placement tolerance of 0.9 nm. Magnetic coercivity and switching field distribution width were measured from polar magneto-optic micro Kerr effect hysteresis loops (with a spot size of 20–50 μm). Patterning process conditions that produced a higher fraction of eroded or merged magnetic islands reduced the BPM coercivity and increased the relative width of the switching field distribution. Magnetic recording was performed with a commercial recording head of magnetic write width 90 nm in a shingled writing method. The recording error rate minimum varied with the fraction of defects in a similar manner as the magnetic switching field distribution width. A higher fraction of defects resulted in increased recording error probability due to data erasure by stray magnetic fields from the head.
In vitro evaluation of the imaging accuracy of C‐arm conebeam CT in cerebral perfusion imaging
Authors: Ganguly A. , Fieselmann A. , Boese J. , Rohkohl C. , Hornegger J. , Fahrig R.
Published: October 2012

Purpose:

The authors have developed a method to enable cerebral perfusion CT imaging using C‐arm based conebeam CT (CBCT). This allows intraprocedural monitoring of brain perfusion during treatment of stroke. Briefly, the technique consists of acquiring multiple scans (each scan comprised of six sweeps) acquired at different time delays with respect to the start of the x‐ray contrast agent injection. The projections are then reconstructed into angular blocks and interpolated at desired time points. The authors have previously demonstrated its feasibilityin vivo using an animal model. In this paper, the authors describe an in vitro technique to evaluate the accuracy of their method for measuring the relevant temporal signals.

Methods:

The authors’ evaluation method is based on the concept that any temporal signal can be represented by a Fourier series of weighted sinusoids. A sinusoidal phantom was developed by varying the concentration of iodine as successive steps of a sine wave. Each step corresponding to a different dilution of iodine contrast solution contained in partitions along a cylinder. By translating the phantom along the axis at different velocities, sinusoidal signals at different frequencies were generated. Using their image acquisition and reconstruction algorithm, these sinusoidal signals were imaged with a C‐arm system and the 3D volumes were reconstructed. The average value in a slice was plotted as a function of time. The phantom was also imaged using a clinical CT system with 0.5 s rotation. C‐arm CBCT results using 6, 3, 2, and 1 scan sequences were compared to those obtained using CT. Data were compared for linear velocities of the phantom ranging from 0.6 to 1 cm/s. This covers the temporal frequencies up to 0.16 Hz corresponding to a frequency range within which 99% of the spectral energy for all temporal signals in cerebral perfusion imaging is contained.

Results

: The errors in measurement of temporal frequencies are mostly below 2% for all multiscan sequences. For single scan sequences, the errors increase sharply beyond 0.10 Hz. The amplitude errors increase with frequency and with decrease in the number of scans used.

Conclusions:

Our multiscan perfusion CT approach allows low errors in signal frequency measurement. Increasing the number of scans reduces the amplitude errors. A two‐scan sequence appears to offer the best compromise between accuracy and the associated total x‐ray and iodine dose.
Development of a flexible optical fiber based high resolution integrated PET/MRI system
Authors: Yamamoto Seiichi , Watabe Hiroshi , Kanai Yasukazu , Watabe Tadashi , Aoki Masaaki , Sugiyama Eiji , Kato Katsuhiko , Hatazawa Jun
Published: October 2012

Purpose:

The simultaneous measurement of PET and magnetic resonance imaging (MRI) is an emerging field for molecular imaging research. Although optical fiber based PET/MRI systems have advantages on less interference between PET and MRI, there is a drawback in reducing the scintillation light due to the fiber. To reduce the problem, the authors newly developed flexible optical fiber bundle based block detectors and employed them for a high resolution integrated PET/MRI system.

Methods:

The flexible optical fiber bundle used 0.5 mm diameter, 80 cm long double clad fibers which have dual 12 mm × 24 mm rectangular inputs and a single 24 mm × 24 mm rectangular output. In the input surface, LGSO scintillators of 0.025 mol.% (decay time: ∼31 ns: 0.9 mm × 1.3 mm × 5 mm) and 0.75 mol.% (decay time: ∼46 ns: 0.9 mm × 1.3 mm × 6 mm) were optically coupled in depth direction to form depth‐of‐interaction detector, arranged in 11 × 13 matrix and optically coupled to the fiber bundle. The two inputs of the bundle are bent for 90°, bound to one, and are optically coupled to a Hamamatsu 1‐in. square position sensitive photomultiplier tube.

Results:

Light loss due to the fiber bundle could be reduced and the performance of the block detectors was improved. Eight optical fiber based block detectors (16 LGSO blocks) were arranged in a 56 mm diameter ring to form a PET system. Spatial resolution and sensitivity were 1.2 mm full‐width at half‐maximum and 1.2% at the central field‐of‐view, respectively. Sensitivity change was less than 1% for 2 °C temperature changes. This PET system was integrated with a 0.3 T permanent magnet MRI system which has 17 cm diameter hole at the yoke area for insertion of the PET detector ring. There was no observable interference between PET and MRI. Simultaneous imaging of PET and MRI was successfully performed for small animal studies.

Conclusions:

The authors confirmed that the developed high resolution PET/MRI system is promising for molecular imaging research.
Dosimetric measurements of Onyx embolization material for stereotactic radiosurgery
Authors: Roberts Donald A. , Balter James M. , Chaudhary Neeraj , Gemmete Joseph J. , Pandey Aditya S.
Published: October 2012

Purpose:

Arteriovenous malformations are often treated with a combination of embolization and stereotactic radiosurgery. Concern has been expressed in the past regarding the dosimetric properties of materials used in embolization and the effects that the introduction of these materials into the brain may have on the quality of the radiosurgery plan. To quantify these effects, the authors have taken large volumes of Onyx 34 and Onyx 18 (ethylene‐vinyl alcohol copolymer doped with tantalum) and measured the attenuation and interface effects of these embolization materials.

Methods:

The manufacturer provided large cured volumes (∼28 cc) of both Onyx materials. These samples were 8.5 cm in diameter with a nominal thickness of 5 mm. The samples were placed on a block tray above a stack of solid water with an Attix chamber at a depth of 5 cm within the stack. The Attix chamber was used to measure the attenuation. These measurements were made for both 6 and 16 MV beams. Placing the sample directly on the solid water stack and varying the thickness of solid water between the sample and the Attix chamber measured the interface effects. The computed tomography (CT) numbers for bulk material were measured in a phantom using a wide bore CT scanner.

Results:

The transmission through the Onyx materials relative to solid water was approximately 98% and 97% for 16 and 6 MV beams, respectively. The interface effect shows an enhancement of approximately 2% and 1% downstream for 16 and 6 MV beams. CT numbers of approximately 2600–3000 were measured for both materials, which corresponded to an apparent relative electron density (RED) to water of approximately 2.7–2.9 if calculated from the commissioning data of the CT scanner.

Conclusions:

We performed direct measurements of attenuation and interface effects of Onyx 34 and Onyx 18 embolization materials with large samples. The introduction of embolization materials affects the dose distribution of a MV therapeutic beam, but should be of negligible consequence for effective thicknesses of less than 8 mm. The measured interface effects are also small, particularly at 6 MV. Large areas of high‐density artifacts and low‐density artifacts can cause errors in dose calculations and need to be identified and resolved during planning.
Monte Carlo performance on the x‐ray converter thickness in digital mammography using software breast models
Authors: Liaparinos P. , Bliznakova K.
Published: October 2012

Purpose:

In x‐ray mammography, some of the components that play significant role to early diagnosis are the x‐ray source, the breast composition as well as the composition of the x‐ray converter. Various studies have previously investigated separately the influence of breast characteristics and detector configuration on the optimization of mammographic imaging systems. However, it is important to examine the combined effect of both components in improving the signal transfer properties in mammography systems of the mammograms. In the present study, the authors compared and evaluated x‐ray converters using software breast models and realistic mammographic spectra in terms of: (a) zero‐frequency detective quantum efficiency (DQE) and (b) sensitivity. The impact of x‐ray converter thickness on contrast threshold (CTH) for observer assessment, based on the Rose model, was demonstrated as well.

Methods:

Monte Carlo techniques were applied to simulate the x‐ray interactions within the software breast phantoms and thereafter within the detective medium. Simulations involved: (a) two mammographic x‐ray spectra: 28 kV Mo, 0.030 mm Mo, and 32 kV W, 0.050 mm Rh of different entrance surface air kerma (ESAK: 3–7 mGy), (b) realistic breast models (dense and fatty) and (c) x‐ray converter materials most frequently considered in investigations on energy integrating digital mammography detectors: the Gd2O2S:Tb granular phosphor, the CsI:Tl structured phosphor, and the a‐Se photoconductive layer. Detector material thickness was considered to vary in the range from 50 mg/cm2 up to 150 mg/cm2.

Results:

The Monte Carlo study showed that: (a) the x‐ray beam becomes less penetrating after passing through dense breasts leading to higher values of zero‐frequency DQE of the x‐ray imaging converters and improved CTH values in all cases considered, (b) W/Rh target/filter combination results in improved CTH values at higher ESAK values, and (c) a‐Se shows higher zero‐frequency DQE values than the phosphor‐based converters, Gd2O2S:Tb and CsI:Tl. However, thicker layers of CsI:Tl could be comparable to a‐Se layers achieving approximately 27.6% CTH improvement at a thickness of 150 mg/cm2.

Conclusions:

The present Monte Carlo investigation indicates that in the energy range employed in mammography, an upper limit, approximately 100 mg/cm2, should be considered in the development of thicker a‐Se converters. On the other hand, above this thickness value, CsI:Tl converter could improve its imaging performance.
Role of Defective Thymic Function in Onset of Ganciclovir-Resistant Cytomegalovirus after Cord Blood Transplantation
Authors: Cantisán Sara , Martín Carmen , Romero-Sánchez María C. , Ferrando-Martínez Sara , Martínez Francisco , Rivero Antonio , Torres Antonio , Solana Rafael , Torre-Cisneros Julián
Published: October 2012

A case of recurrent cytomegalovirus reactivations in a cytomegalovirus-seropositive woman who received allogeneic cord blood transplantation is described. Thirteen months posttransplantation, her CD3
+
T cell count was extremely low whereas natural killer cells represented 66% of her total lymphocytes. She showed defective thymic function that might contribute to the onset of valganciclovir resistance.
Expression of Tumor Necrosis Factor Alpha-Induced Protein 3 mRNA in Peripheral Blood Mononuclear Cells Negatively Correlates with Disease Severity in Psoriasis Vulgaris
Authors: Jiang Xuebing , Tian Hongqing , Fan Yuchen , Chen Jie , Song Yonghong , Wang Shurong , Zhu Faliang , Guo Chun , Zhang Lining , Shi Yongyu
Published: October 2012

Psoriasis vulgaris is considered a chronic inflammatory disease, but its immunopathogenesis has not been well understood. The tumor necrosis factor alpha-induced protein 3 (TNFAIP3) gene functions in negative-feedback regulation of inflammation, and its single nucleotide polymorphism is associated with psoriasis. However, the relationship between the expression level of the TNFAIP3 gene in immune cells and psoriasis is not known so far. In the present study, TNFAIP3 mRNA expression levels in peripheral blood mononuclear cells from 44 patients with psoriasis vulgaris and 30 healthy controls were determined using real-time reverse transcription-PCR analysis. We found that expression of TNFAIP3 mRNA in all patients negatively correlated with the psoriatic area and severity index (PASI) (
r
= −0.5126;
P
= 0.0004) as well as with the percentage of body surface area affected by psoriasis (
r
= −0.5013;
P
= 0.0005). Patients were divided into mild and severe groups based on the mean PASI score. Expression of TNFAIP3 mRNA in the mild group was higher than that in the severe group (
P
= 0.0064). Moreover, compared with that in healthy controls, the expression of TNFAIP3 mRNA in the mild group was significantly upregulated (
P
= 0.0004), but the expression of TNFAIP3 mRNA in the severe group was not. These results suggest that the expression level of TNFAIP3 plays an important role in the pathology of psoriasis vulgaris and that the loss of upregulation of TNFAIP3 expression may contribute to the severity of psoriasis vulgaris.
The natural history of early-onset dementia: the Artemis Project
Authors: Atkins Emily R , Bulsara Max K , Panegyres Peter K
Published: October 2012

Objectives

The natural history of early-onset Alzheimer's disease (AD) and fronto-temporal dementia (FTD) remains to be described in detail. We seek to describe the natural history of early onset AD and FTD in terms of changes in cognitive assessment and staging, medical history and survival.

Design

Longitudinal prospective cohort analysis.

Setting

Neurodegenerative disorders research clinic.

Participants

In total, 155 consecutive patients with clinically confirmed sporadic early-onset AD or FTD at a neurodegenerative disorders research clinic in Subiaco, Western Australia (The Artemis Project).

Methods

A detailed history was recorded from the patients at baseline, including education, family history and medical history. Mini-mental state exam (MMSE), Global Deterioration Scale (GDS) and total functional capacity (TFC) were determined at each visit from 1994 until 2011. Kaplan-Meier survival analysis was performed.

Results

Patients with FTD were more likely to have a family history of dementia (p=0.026), to develop at least one cerebrovascular risk factor (p=0.003), manifest depression (Fisher's exact p=0.007) and to die during the follow-up period (Pearson χ28.97, p=0.003). Kaplan-Meier survival estimates revealed a highly significant difference in the proportion of patients surviving the follow-up period (log rank 7.25, p=0.007) with FTD patients experiencing poorer survival than those with AD. The mean MMSE and TFC were consistently lower in those with FTD compared with those with AD over a decade of follow-up; mean GDS was consistently higher in those with FTD over the follow-up period.

Conclusions

We believe that the difference in survival in patients with AD and FTD in our cohort might relate to the development of one or more cerebrovascular risk factors in FTD patients and the severity of the underlying pathology.
Use of in situ simulation and human factors engineering to assess and improve emergency department clinical systems for timely telemetry-based detection of life-threatening arrhythmias
Authors: Kobayashi Leo , Parchuri Ramakrishna , Gardiner Fenwick G , Paolucci Gino A , Tomaselli Nicole M , Al-Rasheed Rakan S , Bertsch Karina S , Devine Jeffrey , Boss Robert M , Gibbs Frantz J , Goldlust Eric , Monti James E , O'Hearn Brian , Portelli David C , Siegel Nathan A , Hemendinger David , Jay Gregory D
Published: October 2012

Background and objectives

Medical simulation and human factors engineering (HFE) may help investigate and improve clinical telemetry systems. Investigators sought to (1) determine the baseline performance characteristics of an Emergency Department (ED) telemetry system implementation at detecting simulated arrhythmias and (2) improve system performance through HFE-based intervention.

Methods

The prospective study was conducted in a regional referral ED over three 2-week periods from 2010 to 2012. Subjects were clinical providers working at the time of unannounced simulation sessions. Three-minute episodes of sinus bradycardia (SB) and of ventricular tachycardia (VT) were simulated. An experimental HFE-based multi-element intervention was developed to (1) improve system accessibility, (2) increase system relevance and utility for ED clinical practice and (3) establish organisational processes for system maintenance and user base cultivation. The primary outcome variable was overall simulated arrhythmia detection. Pre-intervention system characterisation, post-intervention end-user feedback and real-world correlates of system performance were secondary outcome measures.

Results

Baseline HFE assessment revealed limited accessibility, suboptimal usability, poor utility and general neglect of the telemetry system; one simulated VT episode (5%) was detected during 20 pre-intervention sessions. Systems testing during intervention implementation recorded detection of 4 out of 10 arrhythmia simulations (p=0.03). Twenty post-intervention sessions revealed more VT detections (8 of 10) than SB detections (3 of 10) for a 55% overall simulated arrhythmia detection rate (p=0.001).

Conclusions

Experimental investigations helped reveal and mitigate weaknesses in an ED clinical telemetry system implementation. In situ simulation and HFE methodologies can facilitate the assessment and abatement of patient safety hazards in healthcare environments.
Setting up and running an e‐mail list for your practice
Authors: Barrand Keith
Published: October 2012

Creating an e‐mail list can furnish your practice with a valuable tool for both client education and advertising. It is a cost‐effective and practical alternative to traditional, paper‐based material. Keith Barrand goes through the steps of creating an e‐mail list, and gives advice on collecting addresses, managing the database, e‐mail content and legal considerations.
Grey squirrel treatment and hand‐rearing
Authors: Cousquer Glen
Published: October 2012

An adult female grey squirrel (Sciurus carolinensis) is brought into your veterinary practice together with her unweaned young after their drey was, apparently, blown from a tree. The member of the public who found the squirrels only did so because her dog caught and injured the mother. A brief clinical examination found the mother to be distressed, tachypnoeic and unable to stand; a conscious radiograph identifies a vertebral fracture. The kits are all lively, keen to suckle and one of your nurses is equally keen to hand‐rear them. How should you proceed?