bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross‐species testing of 27 pre‐existing microsatellites in Podarcis gaigeae and Podarcis hispanica (Squamata: Lacertidae)
Authors: RUNEMARK ANNA , GABIROT MARIANNE , BENSCH STAFFAN , SVENSSON ERIK I. , MARTÍN JOSÉ , PAFILIS PANAYIOTIS , VALAKOS EFSTRATIOS D. , HANSSON BENGT 
Published: August 2009

AbstractWe tested 27 microsatellite loci for cross‐species amplification in the lacertids Podarcis gaigeae and Podarcis hispanica. We detected 11 and 15 polymorphic loci in the former and the latter species, respectively. In a larger sample of individuals from a single population of each species, the number of alleles ranged from five to 23 in 10 of the polymorphic loci in P. gaigeae, and between four and 13 in nine of polymorphic loci in P. hispanica. Two locus deviated from Hardy‐Weinberg equilibrium in P. hispanica. Between 11 and 16 of the 27 loci also amplified successfully in three other Podarcis species.
Isolation of polymorphic microsatellite loci for the marine invader Microcosmus squamiger (Ascidiacea)
Authors: RIUS MARC , TURON XAVIER , PASCUAL MARTA 
Published: August 2009

AbstractThe ascidian Microcosmus squamiger is native to Australia and has recently spread worldwide. It has become a pest in some littoral communities within its introduced range. An enriched genomic library of M. squamiger resulted in a total of eight polymorphic loci that were genotyped in 20 individuals from a population within its introduced range, and 20 individuals more from a native population. The mean number of alleles per locus was 5.33 and mean observed heterozygosity was 0.432. No significant linkage disequilibrium was found among loci pairs. Significant genetic differentiation was observed between populations.
Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L.)
Authors: SKIRNISDOTTIR SIGURLAUG , PAMPOULIE CHRISTOPHE , HAUKSDOTTIR SIGURBJORG , SCHULTE INGA , OLAFSSON KRISTINN , HREGGVIDSSON GUDMUNDUR O. , HJORLEIFSDOTTIR SIGRIDUR 
Published: August 2009

AbstractEighteen new microsatellite loci consisting of 10 di‐, 5 tri‐, 2 tetra‐ and 1 heptanucleotide repeats are introduced for the Atlantic cod (Gadus morhua L.). All loci were co‐amplified in two polymerase chain reactions (plus two previously published microsatellites) and all products were typed clearly. The number of alleles per locus ranged from six (PGmo130) to 45 (PGmo76) and the observed heterozygosity ranged from 0.356 (PGmo130) to 0.957 (PGmo95). All loci except one followed Hardy–Weinberg expectations. Genetic linkage disequilibrium analysis between all pairs of loci did not yield any significant values.
Polymorphic microsatellite markers for the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae), a vector of human African trypanosomiasis
Authors: BROWN J. E. , KOMATSU K. J. , ABILA P. P. , ROBINSON A. S. , OKEDI L. M. A. , DYER N. , DONNELLY M. J. , SLOTMAN M. A. , CACCONE A. 
Published: August 2009

AbstractOur understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan population, averaged 0.57, with only two loci showing very low heterozygosity. Five loci carried more than six alleles. Together with five recently published microsatellite loci, this brings the number of available microsatellite loci for this species to 15. Their availability will greatly facilitate future studies on the genetics of this important human disease vector.
Efficient molecular sexing in dioecious Silene latifolia and S. dioica and paternity analysis in F1 hybrids
Authors: HOBZA R , WIDMER A 
Published: August 2009

AbstractTwo polymerase chain reaction‐based assays have been developed that work in combination with an efficient DNA extraction protocol to rapidly and reliably determine sex in the dioecious plant species Silene latifolia and S. dioica. In addition, one of the assays allows assessing paternity in the F1 generation of intra‐ and interspecific matings involving the two species.
Isolation and characterization of 12 microsatellites from the black surfperch, Embiotoca jacksoni, a reef fish that lacks a pelagic larval phase
Authors: BERNARDI GIACOMO 
Published: August 2009

AbstractA set of 12 microsatellite markers was developed from Embiotoca jacksoni genomic DNA and tested for polymorphism using 64 individuals from two populations. All loci were polymorphic with a number of alleles ranging from two to 19 with expected heterozygosities ranging from 0.17 to 0.89. There was no evidence of linkage disequilibrium and all loci were in Hardy–Weinberg equilibrium, except for four loci in one population. High numbers of private alleles were consistent with strong population structure, and very limited dispersal. Six microsatellite markers successfully cross amplified and were polymorphic in closely related species, Embiotoca lateralis and Hyspurus caryi.
Polymorphic microsatellite DNA markers for Banksia hookeriana (Proteaceae)
Authors: HE TIANHUA , KRAUSS SIEGFRIED L. , LAMONT BYRON B. 
Published: August 2009

AbstractWe developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia hookeriana (Proteaceae). The number of alleles per locus in 37 individuals varied from three to 17, observed and expected heterozygosities ranged from 0.297 to 0.838 and from 0.279 to 0.900, respectively. Two loci (BH‐B5 and BH‐B107) showed significant deviation from Hardy–Weinberg equilibrium (P < 0.05), and null alleles may be present at these two loci. All loci showed independent inheritance.
Microsatellite primers for relatedness and population structure in great frigatebirds (Pelecaniformes: Fregatidae)
Authors: DEARBORN DONALD C. , HAILER FRANK , FLEISCHER ROBERT C. 
Published: August 2009

AbstractEighteen moderately polymorphic microsatellite loci were isolated and characterized for great frigatebirds Fregata minor. Polymorphism for the 12 dinucleotide and six tetranucleotide markers was assessed in 23 birds from a Hawaii population. Allelic diversity ranged from two to 12 (mean 5.9), with observed heterozygosity from 0.304 to 0.956 (mean 0.637). Three loci showed homozygote excess, possibly due to null alleles. One additional pair of loci exhibited strong gametic disequilibrium. Thus, at least 14 loci will be useful for studies of relatedness and population structure.
Isolation and characterization of 10 highly polymorphic di‐ and trinucleotide microsatellite markers in the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)
Authors: THEISSINGER KATHRIN , FELDHEIM KEVIN A. , TAUBMANN JULIA , SEITZ ALFRED , PAULS STEFFEN U. 
Published: August 2009

AbstractWe describe the isolation of ten polymorphic microsatellite loci from the mayfly Ameletus inopinatus. Loci had di‐ or trinucleotide repeat motifs and were highly variable with three to 17 alleles (mean = 7.15). Observed heterozygosity ranged from 0.143 to 0.905. One locus (Ami_202) showed significant deviation from Hardy–Weinberg equilibrium in one population, but no evidence for null alleles. One locus (Ami_73) was significantly linked with three other loci. The remaining nine loci should prove highly informative for population genetic studies.
Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary
Authors: Moussard Hélène , Stralis‐Pavese Nancy , Bodrossy Levente , Neufeld Josh D. , Murrell J. Colin 
Published: August 2009

SummaryMethylotrophs play an essential role in the global carbon cycle due to their participation in methane oxidation and C1 metabolism. Despite this important biogeochemical role, marine and estuarine microorganisms that consume C1 compounds are poorly characterized. In this study, we investigated the diversity of active methylotrophs and methanotrophs in sediment from the Colne Estuary (Brightlingsea, UK). Aerobic surface sediment samples were examined for the presence of C1‐utilizing communities using DNA stable‐isotope probing (DNA‐SIP) with 13C‐labelled methane, methanol and monomethylamine. Active methylotrophic bacteria were confirmed after DNA‐SIP and denaturing gradient gel electrophoresis analyses. Clone libraries of 16S rRNA gene amplicons revealed the presence of methylotrophic bacteria affiliated with Methylophaga spp. in methanol and monomethylamine incubations. The addition of marine ammonium mineral salts medium to the microcosms increased the rate of substrate metabolism in DNA‐SIP incubations, although nutrient addition did not affect the active populations contributing 13C‐labelled DNA. The 13CH4 SIP incubations indicated the predominant activity of type I methanotrophs and microarray hybridization of amplified particulate methane monooxygenase (pmoA) genes confirmed the role of type Ia methanotrophs in SIP incubations. Type II methanotrophs (i.e. Methylocystis and Methylosinus) were only detected in the original sediment and in the unlabelled DNA fractions, which indicated that type II methanotrophs were not actively involved in C1 compound assimilation in DNA‐SIP incubations with estuarine surface sediment samples.
A general profile for the MerR family of transcriptional regulators constructed using the semi‐automated Provalidator tool
Authors: Molina‐Henares Antonio J. , Godoy Patricia , Duque Estrella , Ramos Juan L. 
Published: August 2009

SummaryProvalidator is a web‐based tool that facilitates the design and validation of generalized profiles of protein families in prokaryotes. This tool combines the nearly full automation of profile building with a search for family members in all available databases. The tool is useful for assigning a given protein to a specific family, and is also useful for genome mining in annotated prokaryotic genomes. The tool is freely available at http://www.bactregulators.org. As proof of concept we constructed a profile that best defines the MerR family of transcriptional regulators. The profile created includes functional residues that are part of the helix–turn–helix DNA binding domain and accessory elements defined as wings 1 and 2, suggesting that members of the MerR family of regulators may exhibit conserved 3D structure in the region that defines the family profile. The profile defined for MerR was used to search for members of this family in the Swiss‐Prot and TrEMBL databases, and also to identify members of the family in the genome of Pseudomonas putida. One of these identified regulators was found to be involved in zinc tolerance, showing the usefulness of identifying family members and assigning phenotypes.
An evaluation of bovine derived xenograft with and without a bioabsorbable collagen membrane in the treatment of mandibular Class II furcation defects
Authors: Taheri M , Molla R , Radvar M , Sohrabi K , Najafi MH 
Published: August 2009

AbstractBackground:  The aim of this study was to compare the clinical outcomes of applying Bio‐Oss®, an anorganic bovine bone xenograft (control group) to the combined use of Bio‐Oss® and Bio‐Gide® (a bioabsorbable collagen membrane) (test group) in human mandibular Class II furcation defects.Methods:  A total of 18 furcations (8 tests and 10 controls) in 14 patients suffering from chronic periodontitis were treated in this randomized clinical trial. Open vertical and horizontal furcation depths (OVFD and OHFD), vertical and horizontal clinical attachment levels (VCAL, HCAL), probing depth (PD) and free gingival marginal level (GML) were among the clinical parameters measured prior and six months after treatment, at re‐entry surgery. The data were analysed by statistical tests while a p value less than 0.05 was considered significant.Results:  At the surgical re‐entry, the mean reduction for OVFD of the control and test groups was 1.9 ± 1.3 and 2.1 ± 1.0, and for OHFD 2.1 ± 0.7 and 2.4 ± 1.3, respectively. The control and test treatments resulted in significant reductions in PD, VCAL and HCAL measurements at re‐entry but there was no statistically significant difference between the two treatments in all soft and hard tissues measurements.Conclusions:  This clinical trial failed to demonstrate the superiority of the combined use of Bio‐Gide® and Bio‐Oss® to the use of Bio‐Oss® alone, although both therapies resulted in significant gains in attachment level and bone fill.
Simplified “on‐couch” daily quality assurance procedure for CT simulators
Authors: Liu Ruijie Rachel , Prado Karl , Gillin Michael 
Published: August 2009

For most computed tomography (CT) simulators, radiation therapists must first remove the fat couch top in order to perform daily CT quality assurance (QA), and then use separate tools to perform localization‐laser QA. This process wastes time and effort, and creates the opportunity for accidents to occur. In this study, we tested a simple, yet comprehensive, daily QA program and phantom designed for CT simulators used in radiation oncology that would enable us to use only one tool to perform both laser and imaging QA on a fat couch. To construct a modified QA phantom, we attached three adjustable legs and fastened two metric scales (one vertically and one horizontally) to a commercial CT QA phantom. The adjustable legs helped to position and level the phantom conveniently in the needed position. The two metric scales were used for localization‐laser QA, while the phantom body was used for CT imaging QA. We evaluated five different CT scanners from two manufacturers with their designated couches to evaluate this phantom system. Since the couch is scanned along with the phantom, we evaluated the couch's effect on image quality. We found that the presence of the couch top changed the uniformity of water's CT number slightly, but did not change the visual image resolution. The couch top also produced different, yet reproducible, effects on image quality. The effects were greatest in the section of the phantom closest to the couch top. For a commercial carbon fiber couch top, the variation was within 3 Hounsfield Units (HU). The effect was couch‐ and scanner‐specific, and could be incorporated into the QA acceptability criteria for each CT scanner. By using the proposed QA program and phantom, we have been able to implement more thorough QA while decreasing the amount of effort and time the simulation therapists spend performing laser and imaging QA.PACS number(s): 87.55.Gh, 87.55.Qr, 87.56.Fc, 87.57.Q‐
Application of holographic display in radiotherapy treatment planning II: a multi‐institutional study
Authors: Chu James C H , Gong Xing , Cai Yang , Kirk Michael C , Zusag Thomas W , Shott Susan , Rivard Mark J , Melhus Christopher S , Cardarelli Gene A , Hurley Amanda , Hepel Jaroslaw T , Napoli Josh , Stutsman Sandy , Abrams Ross A 
Published: August 2009

We hypothesized that use of a true 3D display providing easy visualization of patient anatomy and dose distribution would lead to the production of better quality radiation therapy treatment plans. We report on a randomized prospective multi‐institutional study to evaluate a novel 3D display for treatment planning.The Perspecta® Spatial 3D System produces 360° holograms by projecting cross‐sectional images on a diffuser screen rotating at 900 rpm. Specially‐developed software allows bi‐directional transfer of image and dose data between Perspecta and the Pinnacle planning system.Thirty‐three patients previously treated at three institutions were included in this IRB‐approved study. Patient data were de‐identified, randomized, and assigned to different planners. A physician at each institution reviewed the cases and established planning objectives. Two treatment plans were then produced for each patient, one based on the Pinnacle system alone and another in conjunction with Perspecta. Plan quality was then evaluated by the same physicians who established the planning objectives. All plans were viewable on both Perspecta and Pinnacle for review. Reviewing physicians were blinded to the planning device used. Data from a 13‐patient pilot study were also included in the analysis.Perspecta plans were considered better in 28 patients (61%), Pinnacle in 14 patients (30%), and both were equivalent in 4 patients. The use of non‐coplanar beams was more common with Perspecta plans (82% vs. 27%). The mean target dose differed by less than 2% between rival plans. Perspecta plans were somewhat more likely to have the hot spot located inside the target (43% vs. 33%). Conversely, 30% of the Pinnacle plans had the hot spot outside the target compared with 18% for Perspecta plans. About 57% of normal organs received less dose from Perspecta plans. No statistically significant association was found between plan preference and planning institution or planner.The study found that use of the holographic display leads to radiotherapy plans preferred in a majority of cases over those developed with 2D displays. These data indicate that continued development of this technology for clinical implementation is warranted.PACS numbers: 87.55.D
Construction of anthropomorphic phantoms for use in dosimetry studies
Authors: Winslow James F. , Hyer Daniel E. , Fisher Ryan F. , Tien Christopher J. , Hintenlang David E. 
Published: August 2009

This paper reports on the methodology and materials used to construct anthropomorphic phantoms for use in dosimetry studies, improving on methods and materials previously described by Jones et al. [Med Phys. 2006;33(9):3274–82]. To date, the methodology described has been successfully used to create a series of three different adult phantoms at the University of Florida (UF). All phantoms were constructed in 5 mm transverse slices using materials designed to mimic human tissue at diagnostic photon energies: soft tissue‐equivalent substitute (STES), lung tissue‐equivalent substitute (LTES), and bone tissue‐equivalent substitute (BTES). While the formulation for BTES remains unchanged from the previous epoxy resin compound developed by Jones et al. [Med Phys. 2003;30(8):2072—81], both the STES and LTES were redesigned utilizing a urethane‐based compound which forms a pliable tissue‐equivalent material. These urethane‐based materials were chosen in part for improved phantom durability and easier accommodation of real‐time dosimeters. The production process has also been streamlined with the use of an automated machining system to create molds for the phantom slices from bitmap images based on the original segmented computed tomography (CT) datasets. Information regarding the new tissue‐equivalent materials, as well as images of the construction process and completed phantom, are included.PACS number: 87.53.Bn
eIMRT: a web platform for the verification and optimization of radiation treatment plans
Authors: Pena Javier , González‐Castaño Diego M , Gómez Faustino , Gago‐Arias Araceli , González‐Castaño Francisco J. , Rodríguez‐Silva Daniel , Gómez Andrés , Mouriño Carlos , Pombar Miguel , Sánchez Manuel 
Published: August 2009

The eIMRT platform is a remote distributed computing tool that provides users with Internet access to three different services: Monte Carlo optimization of treatment plans, CRT & IMRT treatment optimization, and a database of relevant radiation treatments/clinical cases. These services are accessible through a user‐friendly and platform independent web page. Its flexible and scalable design focuses on providing the final users with services rather than a collection of software pieces. All input and output data (CT, contours, treatment plans and dose distributions) are handled using the DICOM format.The design, implementation, and support of the verification and optimization algorithms are hidden to the user. This allows a unified, robust handling of the software and hardware that enables these computation‐intensive services. The eIMRT platform is currently hosted by the Galician Supercomputing Center (CESGA) and may be accessible upon request (there is a demo version at http://eimrt.cesga.es:8080/eIMRT2/demo; request access in http://eimrt.cesga.es/signup.html).This paper describes all aspects of the eIMRT algorithms in depth its user interface, and its services. Due to the flexible design of the platform, it has numerous applications including the intercenter comparison of treatment planning, the quality assurance of radiation treatments, the design and implementation of new approaches to certain types of treatments, and the sharing of information on radiation treatment techniques.In addition, the web platform and software tools developed for treatment verification and optimization have a modular design that allows the user to extend them with new algorithms. This software is not a commercial product. It is the result of the collaborative effort of different public research institutions and is planned to be distributed as an open source project. In this way, it will be available to any user; new releases will be generated with the new implemented codes or upgrades.PACS number: 87.55.kh
Image quality & dosimetric property of an investigational Imaging Beam Line MV‐CBCT
Authors: Beltran Chris , Lukose Renin , Gangadharan Bijumon , Bani‐Hashemi Ali , Faddegon Bruce A. 
Published: August 2009

To measure and compare the contrast to noise ratio (CNR) as a function of dose for the CBCTs produced by the mega‐voltage (MV) imaging beam line (IBL) and the treatment beam line (TBL), and to compare the dose to target and various critical structures of pediatric patients for the IBL CBCT versus standard TBL orthogonal port films.Two Siemens Oncor linear accelerators were modified at our institution such that the MV‐CBCT would operate under an investigational IBL rather than the standard 6MV TBL. Prior to the modification, several CBCTs of an electron density phantom were acquired with the TBL at various dose values. After the modification, another set of CBCTs of the electron density phantom were acquired for various doses using the IBL. The contrast to noise ratio (CNR) for each tissue equivalent insert was calculated. In addition, a dosimetric study of pediatric patients was conducted comparing the 1 cGy IBL CBCT and conventional TBL orthogonal pair port films.The CNR for eight tissue equivalent inserts at five different dose settings for each type of CBCT was measured. The CNR of the muscle insert was 0.8 for a 5 cGy TBL CBCT, 1.1 for a 1.5 cGy IBL CBCT, and 2.8 for a conventional CT. The CNR of the trabecular bone insert was 2.9 for a 5 cGy TBL CBCT, 5.5 for a 1.5 cGy IBL CBCT, and 14.8 for a conventional CT. The IBL CBCT delivered approximately one‐fourth the dose to the target and critical structures of the patients as compared to the TBL orthogonal pair port films.The IBL CBCT improves image quality while simultaneously reducing the dose to the patient as compared to the TBL CBCT. A 1 cGy IBL CBCT, which is used for bony anatomy localization, delivers one‐fourth the dose as compared to conventional ortho‐pair films.PACS number: 87.57.Q, 87.57.cj, 87.53.Jw