bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular analysis of immunized Jr(a–) or Lan– patients and validation of a high‐throughput genotyping assay to screen blood donors for Jr(a–) and Lan– phenotypes
Authors: Haer‐Wigman Lonneke , Ait Soussan Aïcha , Ligthart Peter , de Haas Masja , van der Schoot C. Ellen 
Published: January 2014

BackgroundIndividuals with anti‐Jra or anti‐Lan are ideally transfused with rare Jr(a–) or Lan– red blood cells. We characterized mutations in Dutch Jr(a–) and Lan– individuals and developed a high‐throughput genotyping assay to detect Jr(a–) and Lan– donors.Study Design and MethodsSix Jr(a–) and seven Lan– persons, who all made anti‐Jra or anti‐Lan, were sequenced for ABCG2 or ABCB6 and the copy number of ABCG2 and ABCB6 was determined. A total of 3366 Caucasian, 621 black, and 333 Chinese donors were screened with a high‐throughput screening assay targeting frequently occurring mutations causing the Jr(a–) or Lan– phenotype.ResultsIn the six tested Jr(a–) individuals previously described, c.376C > T, c.706C > T, and c.736C > T nonsense mutations in ABCG2 were detected. In the seven Lan– individuals 12 different mutations, of which 10 underlie the Lan– phenotype, were detected. No copy number variation was detected for ABCG2 and ABCB6. The high‐throughput screening assay detected five Caucasian donors heterozygous for the c.706C > T or 736C > T mutation in ABCG2 and nine Caucasian donors heterozygous for the 574C > T mutation in ABCB6. No black or Chinese donors were found positive for a mutation.ConclusionWe describe eight new mutations in ABCB6 of which seven, including three missense mutations, underlie the Lan– phenotype and determine that a complete gene deletion of ABCG2 or ABCB6 is not responsible for the Jr(a–) or Lan– phenotype, respectively. The extended heterogeneity of mutations causing the Jr(a–) or Lan– phenotype in most populations makes genetic screening for the Jr(a–) and Lan– phenotype inefficient in those populations.
Model‐based dose calculations for COMS eye plaque brachytherapy using an anatomically realistic eye phantom
Authors: Lesperance Marielle , Inglis‐Whalen M. , Thomson R. M. 
Published: January 2014

Purpose: To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with125I, 103Pd, or 131Cs seeds, and to investigate doses to ocular structures.Methods: An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user‐code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG‐43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye.Results: Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG‐43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up to 16%. In the full eye model simulations, the average dose to the lens is larger by 7%–9% than the dose to the center of the lens, and the maximum dose to the optic nerve is 17%–22% higher than the dose to the optic disk for all radionuclides. In general, when normalized to the same prescription dose at the tumor apex, doses delivered to all structures of interest in the full eye model are lowest for103Pd and highest for 131Cs, except for the tumor where the average dose is highest for 103Pd and lowest for 131Cs.Conclusions: The eye is not radiologically water‐equivalent, as doses from simulations of the plaque in the full eye model differ considerably from doses for the plaque in a water phantom and from simulated TG‐43 calculated doses. This demonstrates the importance of model‐based dose calculations for eye plaque brachytherapy, for which accurate elemental compositions of ocular media are necessary.
A Monte Carlo investigation of low‐Z target image quality generated in a linear accelerator using Varianˈs VirtuaLinaca)
Authors: Parsons David , Robar James L. , Sawkey Daren 
Published: January 2014

Purpose:The focus of this work was the demonstration and validation of VirtuaLinac with clinical photon beams and to investigate the implementation of low‐Z targets in a TrueBeam linear accelerator (Linac) using Monte Carlo modeling.Methods:VirtuaLinac, a cloud based web application utilizing Geant4 Monte Carlo code, was used to model the Linac treatment head components. Particles were propagated through the lower portion of the treatment head using BEAMnrc. Dose distributions and spectral distributions were calculated using DOSXYZnrc and BEAMdp, respectively. For validation, 6 MV flattened and flattening filter free (FFF) photon beams were generated and compared to measurement for square fields, 10 and 40 cm wide and at dmax for diagonal profiles. Two low‐Z targets were investigated: a 2.35 MeV carbon target and the proposed 2.50 MeV commercial imaging target for the TrueBeam platform. A 2.35 MeV carbon target was also simulated in a 2100EX Clinac using BEAMnrc. Contrast simulations were made by scoring the dose in the phosphor layer of an IDU20 aSi detector after propagating through a 4 or 20 cm thick phantom composed of water and ICRP bone.Results:Measured and modeled depth dose curves for 6 MV flattened and FFF beams agree within 1% for 98.3% of points at depths greater than 0.85 cm. Ninety three percent or greater of points analyzed for the diagonal profiles had a gamma value less than one for the criteria of 1.5 mm and 1.5%. The two low‐Z target photon spectra produced in TrueBeam are harder than that from the carbon target in the Clinac. Percent dose at depth 10 cm is greater by 3.6% and 8.9%; the fraction of photons in the diagnostic energy range (25–150 keV) is lower by 10% and 28%; and contrasts are lower by factors of 1.1 and 1.4 (4 cm thick phantom) and 1.03 and 1.4 (20 cm thick phantom), for the TrueBeam 2.35 MV/carbon and commercial imaging beams, respectively.Conclusions:VirtuaLinac is a promising new tool for Monte Carlo modeling of novel target designs. A significant spectral difference is observed between the low‐Z target beam on the Clinac platform and the proposed imaging beam line on TrueBeam, with the former providing greater diagnostic energy content.
Development and evaluation of a prototype tracking system using the treatment couch
Authors: Lang Stephanie , Zeimetz Jörg , Ochsner Gregor , Schmid Daners Marianne , Riesterer Oliver , Klöck Stephan 
Published: January 2014

Purpose:Tumor motion increases safety margins around the clinical target volume and leads to an increased dose to the surrounding healthy tissue. The authors have developed and evaluated a one‐dimensional treatment couch tracking system to counter steer respiratory tumor motion. Three different motion detection sensors with different lag times were evaluated.Methods:The couch tracking system consists of a motion detection sensor, which can be the topometrical system Topos (Cyber Technologies, Germany), the respiratory gating system RPM (Varian Medical Systems) or a laser triangulation system (Micro Epsilon), and the Protura treatment couch (Civco Medical Systems). The control of the treatment couch was implemented in the block diagram environment Simulink (MathWorks). To achieve real time performance, the Simulink models were executed on a real time engine, provided by Real‐Time Windows Target (MathWorks). A proportional‐integral control system was implemented. The lag time of the couch tracking system using the three different motion detection sensors was measured. The geometrical accuracy of the system was evaluated by measuring the mean absolute deviation from the reference (static position) during motion tracking. This deviation was compared to the mean absolute deviation without tracking and a reduction factor was defined. A hexapod system was moving according to seven respiration patterns previously acquired with the RPM system as well as according to a sin6 function with two different frequencies (0.33 and 0.17 Hz) and the treatment table compensated the motion.Results:A prototype system for treatment couch tracking of respiratory motion was developed. The laser based tracking system with a small lag time of 57 ms reduced the residual motion by a factor of 11.9 ± 5.5 (mean value ± standard deviation). An increase in delay time from 57 to 130 ms (RPM based system) resulted in a reduction by a factor of 4.7 ± 2.6. The Topos based tracking system with the largest lag time of 300 ms achieved a mean reduction by a factor of 3.4 ± 2.3. The increase in the penumbra of a profile (1 × 1 cm2) for a motion of 6 mm was 1.4 mm. With tracking applied there was no increase in the penumbra.Conclusions:Couch tracking with the Protura treatment couch is achievable. To reliably track all possible respiration patterns without prediction filters a short lag time below 100 ms is needed. More scientific work is necessary to extend our prototype to tracking of internal motion.
Toward optimal organ at risk sparing in complex volumetric modulated arc therapy: An exponential trade‐off with target volume dose homogeneity
Authors: Tol Jim P. , Dahele Max , Doornaert Patricia , Slotman Ben J. , Verbakel Wilko F. A. R. 
Published: January 2014

Purpose:Conventional radiotherapy typically aims for homogenous dose in the planning target volume (PTV) while sparing organs at risk (OAR). The authors quantified and characterized the trade‐off between PTV dose inhomogeneity (IH) and OAR sparing in complex head and neck volumetric modulated arc therapy plans.Methods:Thirteen simultaneous integrated boost plans were created per patient, for ten patients. PTV boost(B)/elective(E) optimization priorities were systematically increased. IHB and IHE, defined as (100% − V95%) + V107%, were evaluated against the average of the mean dose to the combined composite swallowing and combined salivary organs (D‐OARcomp). To investigate the influence of OAR size and position with respect to PTVB/E, OAR dose was evaluated against a modified Euclidean distance (DMB/DME) between OAR and PTV.Results:Although the achievable D‐OARcomp for a given level of PTV IH differed between patients, excellent logarithmic fits described the D‐OARcomp/IHB and IHE relationship in all patients (mean R2 of 0.98 and 0.97, respectively). Allowing an increase in average IHB and IHE over a clinically acceptable range, e.g., from 0.4% ± 0.5% to 2.0% ± 2.0% and 6.9% ± 2.8% to 14.8% ± 2.7%, respectively, corresponded to a decrease in average dose to the composite salivary and swallowing structures from 30.3 ± 6.5 to 23.6 ± 4.7 Gy and 32.5 ± 8.3 to 26.8 ± 9.3 Gy. The increase in PTVE IH was mainly accounted for by an increase in V107, by on average 5.9%, rather than a reduction in V95, which was on average only 2%. A linear correlation was found between the OAR dose to composite swallowing structures and contralateral parotid and submandibular gland, with DME (R2 = 0.83, 0.88, 0.95). Only mean ipsilateral parotid dose correlated with DMB (R2 = 0.87).Conclusions:OAR sparing is highly dependent on the permitted PTVB/E IH. PTVE IH substantially influences OAR doses. These results are relevant for clinical practice and for future automated treatment‐planning strategies.
Muscle Activation Levels of the Gluteus Maximus and Medius During Standing Hip-Joint-Strengthening Exercises Using Elastic-Tubing Resistance
Authors: Youdas James W. , Adams Kady E. , Bertucci John E. , Brooks Koel J. , Nelson Meghan M. , Hollman John H. 
Published: January 2014

Context:No published studies have compared muscle activation levels simultaneously for the gluteus maximus and medius muscles of stance and moving limbs during standing hip-joint strengthening while using elastic-tubing resistance.Objective:To quantify activation levels bilaterally of the gluteus maximus and medius during resisted lower-extremity standing exercises using elastic tubing for the cross-over, reverse cross-over, front-pull, and back-pull exercise conditions.Design:Repeated measures.Setting:Laboratory.Participants:26 active and healthy people, 13 men (25 ± 3 y) and 13 women (24 ± 1 y).Intervention:Subjects completed 3 consecutive repetitions of lower-extremity exercises in random order.Main Outcome Measures:Surface electromyographic (EMG) signals were normalized to peak activity in the maximum voluntary isometric contraction (MVIC) trial and expressed as a percentage. Magnitudes of EMG recruitment were analyzed with a 2 × 4 repeated-measures ANOVA for each muscle (α = .05).Results:For the gluteus maximus an interaction between exercise and limb factor was significant (F3,75 = 21.5; P < .001). The moving-limb gluteus maximus was activated more than the stance limb's during the back-pull exercise (P < .001), and moving-limb gluteus maximus muscle recruitment was greater for the back-pull exercise than for the cross-over, reverse cross-over, and front-pull exercises (P < .001). For the gluteus medius an interaction between exercise and limb factor was significant (F3,75 = 3.7; P < .03). Gluteus medius muscle recruitment (% MVIC) was greater in the stance limb than moving limb when performing the front-pull exercise (P < .001). Moving-limb gluteus medius muscle recruitment was greater for the reverse cross-over exercise than for the cross-over, front-pull, and back-pull exercises (P < .001).Conclusions:From a clinical standpoint there is no therapeutic benefit to selectively activate the gluteus maximus and gluteus medius muscles on the stance limb by resisting sagittal- and frontal-plane hip movements on the moving limb using resistance supplied by elastic tubing.
A Cross-Sectional Study Examining Shoulder Pain and Disability in Division I Female Swimmers
Authors: Harrington Shana , Meisel Corinne , Tate Angela 
Published: January 2014

Context:The prevalence of shoulder pain in the competitive swimming population has been reported to be as high as 91%. Female collegiate swimmers have a reported shoulder-injury rate 3 times greater than their male counterparts. There has been little information on how to best prevent shoulder pain in this population. The purpose of this study was to examine if differences exist in shoulder range of motion, upper-extremity strength, core endurance, and pectoralis minor length in NCAA Division I female swimmers with and without shoulder pain and disability.Methods:NCAA Division I females (N = 37) currently swimming completed a brief survey that included the pain subscale of the Penn Shoulder Score (PSS) and the sports/performing arts module of the Disabilities of the Arm, Shoulder, and Hand (DASH) Outcome Measure. Passive range of motion for shoulder internal rotation (IR) and external rotation (ER) at 90° abduction was measured using a digital inclinometer. Strength was measured using a handheld dynamometer for scapular depression and adduction, scapular adduction, IR, and ER. Core endurance was assessed using the side-bridge and prone-bridge tests. Pectoralis minor muscle length was assessed in both a resting and a stretched position using the PALM palpation meter. All measures were taken on the dominant and nondominant arms.Results:Participants were classified as positive for pain and disability if the following 2 criteria were met: The DASH sports module score was >6/20 points and the PSS strenuous pain score was ≥4/10. If these criteria were not met, participants were classified as negative for pain and disability. Significant differences were found between the 2 groups on the dominant side for pectoralis muscle length at rest (P = .003) and stretch (P = .029).Conclusions:The results provide preliminary evidence regarding an association between a decrease in pectoralis minor length and shoulder pain and disability in Division I female swimmers.
Complete Genome Sequence of Acinetobacter baumannii ZW85-1
Authors: Wang Xin , Zhang Zhewen , Hao Qiong , Wu Jiayan , Xiao Jingfa , Jing Huaiqi 
Published: January 2014

ABSTRACT

Acinetobacter baumannii
is an aerobic, nonmotile Gram-negative bacterium that causes nosocomial infections worldwide. Here, we report the complete genome sequence of
Acinetobacter baumannii
strain ZW85-1 and its two plasmids. One of the plasmids carries genes for NDM-1, which can hydrolyze a wide range of antibiotics.
Genome Sequence of
Bacillus
sp. Strain FJAT-14515
Authors: Liu Guohong , Liu Bo , Tang Weiqi , Che Jianmei , Lin Yingzhi , Zhu Yujing , Su Mingxing , Tang Jianyang 
Published: January 2014

ABSTRACT

We report the draft genome sequence of
Bacillus
sp. strain FJAT-14515. The genome is 5.44 Mb in length. It covers 5,263 genes with an average length of 791 bp, has a G+C value of 37.06%, and contains 67 tRNAs, 31 small RNAs, and 5 rRNA loci.
Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection
Authors: Tielen Petra , Wibberg Daniel , Blom Jochen , Rosin Nathalie , Meyer Ann-Kathrin , Bunk Boyke , Schobert Max , Tüpker Reinhilde , Schatschneider Sarah , Rückert Christian , Albersmeier Andreas , Goesmann Alexander , Vorhölter Frank-Jörg , Jahn Dieter , Pühler Alfred 
Published: January 2014

ABSTRACT

Pseudomonas aeruginosa
is a notable nosocomial pathogen causing severe chronic infections. Here we present the draft genome sequence of
P. aeruginosa
MH27, isolated from a patient with a chronic hospital-acquired catheter-associated urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds contributes to the understanding of biofilm formation and antibiotic resistance.
Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus
Youngiibacter
Authors: Wawrik Colin B. , Callaghan Amy V. , Stamps Blake W. , Wawrik Boris 
Published: January 2014

ABSTRACT

The genome of
Youngiibacter fragilis
, the type strain of the newly described genus
Youngiibacter
, was sequenced. The genome consists of 3.996 Mb, with a G+C content of 46.6 mol%.
Y. fragilis
originates from coal-bed methane-produced water and may provide insight into the microbiological basis of biogas production in coal beds.
Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations
Authors: Baltrus David A. , Yourstone Scott , Lind Abigail , Guilbaud Caroline , Sands David C. , Jones Corbin D. , Morris Cindy E. , Dangl Jeffrey L. 
Published: January 2014

ABSTRACT

Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of
Pseudomonas syringae
, obtained from numerous environmental sources and geographically proximate crop species. Overall, these sequences provide a wealth of information about the differences (or lack thereof) between isolates from disease outbreaks and those from other sources.
Draft Genome Sequence of the
Microbispora
sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107
Authors: Sosio Margherita , Gallo Giuseppe , Pozzi Roberta , Serina Stefania , Monciardini Paolo , Bera Agnieska , Stegmann Evi , Weber Tilmann 
Published: January 2014

ABSTRACT

We report the draft genome sequence of
Microbispora
sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain
Microbispora
sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.
Complete Genome Sequence of Chlamydia trachomatis Ocular Serovar C Strain TW-3
Authors: Borges Vítor , Pinheiro Miguel , Vieira Luís , Sampaio Daniel A. , Nunes Alexandra , Borrego Maria J. , Gomes João P. 
Published: January 2014

ABSTRACT

Chlamydia trachomatis
is the etiological agent of trachoma, the leading infectious cause of blindness worldwide. We report here the first complete and annotated genome of a
C. trachomatis
trachoma-causing serovar C strain (strain TW-3). The chromosome and plasmid are 1,043,554 bp and 7,501 bp in length, respectively.
Draft Genome Sequence of
Marinomonas
sp. Strain D104, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean
Authors: Dong Chunming , Bai Xiuhua , Lai Qiliang , Xie Yanrong , Chen Xin , Shao Zongze 
Published: January 2014

ABSTRACT

Marinomonas
sp. strain D104 was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched from deep-sea sediment from the Arctic Ocean. The draft genome sequence of D104 (approximately 3.83 Mbp) contains 62 contigs and 3,576 protein-encoding genes, with a G+C content of 44.8%.
Genome Sequence of a Helicobacter pylori Strain Isolated from a Mexican Patient with Intestinal Gastric Cancer
Authors: Méndez-Tenorio Alfonso , Larios-Serrato Violeta , Olguín-Ruiz Gabriela Edith , Sánchez-Vallejo Carlos Javier , Torres-López Roberto Carlos , Avilés-Jiménez Francisco , Camorlinga-Ponce Margarita , Torres Javier 
Published: January 2014

ABSTRACT

Helicobacter pylori
strains are the major risk factor for gastric cancer. Strains vary in their content of disease-associated genes, so genome-wide analysis of cancer-isolated strains will help elucidate their pathogenesis and genetic diversity. We present the draft genome sequence of
H. pylori
isolated from a Mexican patient with intestinal gastric cancer.
Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in
rpsL
Conferring Streptomycin Resistance and in the
avrRpt2
Effector Altering Host Interactions
Authors: Smits Theo H. M. , Guerrero-Prieto Víctor M. , Hernández-Escarcega Germán , Blom Jochem , Goesmann Alexander , Rezzonico Fabio , Duffy Brion , Stockwell Virginia O. 
Published: January 2014

ABSTRACT

We report draft genome sequences of three Mexican
Erwinia amylovora
strains. A novel plasmid, pEA78, was identified. Comparative genomics revealed an
rpsL
chromosomal mutation conferring high-level streptomycin resistance in two strains. In the effector gene
avrRpt2
, a single nucleotide polymorphism was detected that overcomes fire blight disease resistance in
Malus
×
robusta
5.
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265
Authors: Eckweiler Denitsa , Bunk Boyke , Spröer Cathrin , Overmann Jörg , Häussler Susanne 
Published: January 2014

ABSTRACT

The evolution of small-colony variants within
Pseudomonas aeruginosa
populations chronically infecting the cystic fibrosis lung is one example of the emergence of adapted subpopulations. Here, we present the complete genome sequence of the autoaggregative and hyperpiliated
P. aeruginosa
small-colony variant SCV20265, which was isolated from a cystic ﬁbrosis (CF) patient.