bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Note: Unified imaging and robotic couch quality assurance
Authors: Cook Molly C. , Roper Justin , Elder Eric S. , Schreibmann Eduard 
Published: August 2016

Purpose:To introduce a simplified quality assurance (QA) procedure that integrates tests for the linac's imaging components and the robotic couch. Current QA procedures for evaluating the alignment of the imaging system and linac require careful positioning of a phantom at isocenter before image acquisition and analysis. A complementary procedure for the robotic couch requires an initial displacement of the phantom and then evaluates the accuracy of repositioning the phantom at isocenter. We propose a two‐in‐one procedure that introduces a custom software module and incorporates both checks into one motion for increased efficiency.Methods:The phantom was manually set with random translational and rotational shifts, imaged with the in‐room imaging system, and then registered to the isocenter using a custom software module. The software measured positioning accuracy by comparing the location of the repositioned phantom with a CAD model of the phantom at isocenter, which is physically verified using the MV port graticule. Repeatability of the custom software was tested by an assessment of internal marker location extraction on a series of scans taken over differing kV and CBCT acquisition parameters.Results:The proposed method was able to correctly position the phantom at isocenter within acceptable 1 mm and 1° SRS tolerances, verified by both physical inspection and the custom software. Residual errors for mechanical accuracy were 0.26 mm vertically, 0.21 mm longitudinally, 0.55 mm laterally, 0.21° in pitch, 0.1° in roll, and 0.67° in yaw. The software module was shown to be robust across various scan acquisition parameters, detecting markers within 0.15 mm translationally in kV acquisitions and within 0.5 mm translationally and 0.3° rotationally across CBCT acquisitions with significant variations in voxel size. Agreement with vendor registration methods was well within 0.5 mm; differences were not statistically significant.Conclusions:As compared to the current two‐step approach, the proposed QA procedure streamlines the workflow, accounts for rotational errors in imaging alignment, and simulates a broad range of variations in setup errors seen in clinical practice.
Estimating scatter in cone beam CT with striped ratio grids: A preliminary investigation
Authors: Hsieh Scott 
Published: August 2016

Purpose:To propose a new method for estimating scatter in x‐ray imaging. Conventional antiscatter grids reject scatter at an efficiency that is constant or slowly varying over the surface of the grid. A striped ratio antiscatter grid, composed of stripes that alternate between high and low grid ratio, could be used instead. Such a striped ratio grid would reduce scatter‐to‐primary ratio as a conventional grid would, but more importantly, the signal discontinuities at the boundaries of stripes can be used to estimate local scatter content.Methods:Signal discontinuities provide information on scatter, but are contaminated by variation in primary radiation. A nonlinear image processing algorithm is used to estimate the scatter content in the presence of primary variation. We emulated a striped ratio grid by imaging phantoms with two sequential CT scans, one with and one without a conventional grid. These two scans are processed together to mimic a striped ratio grid. This represents a best case limit of the striped ratio grid, in that the extent of grid ratio modulation is very high and the scatter contrast is maximized.Results:In a uniform cylinder, the striped ratio grid virtually eliminates cupping. Artifacts from scatter are improved in an anthropomorphic phantom. Some banding artifacts are induced by the striped ratio grid.Conclusions:Striped ratio grids could be a simple and effective evolution of conventional antiscatter grids. Construction and validation of a physical prototype remains an important future step.
Draft Genome Sequence of
Micromonospora
sp
.
Strain HK10, Isolated from Kaziranga National Park, India
Authors: Talukdar Madhumita , Das Dhrubajyoti , Borah Chiranjeeta , Deka Boruah Hari Prasanna , Bora Tarun Chandra , Singh Anil Kumar 
Published: August 2016

ABSTRACT

We report the 6.92-Mbp genome sequence of
Micromonospora
sp. HK10, isolated from soil samples collected from Kaziranga National Park, Assam, India. The full genome of strain
Micromonospora
sp
.
strain HK10 consists of 6,911,179 bp with 73.39% GC content, 6,196 protein-coding genes, and 86 RNAs.
Genome Sequence of
Gordonia
Phage BetterKatz
Authors: Pope Welkin H. , Berryman Emily N. , Forrest Kaitlyn M. , McHale Lilliana , Wertz Anthony T. , Zhuang Zenas , Kasturiarachi Naomi S. , Pressimone Catherine A. , Schiebel Johnathon G. , Furbee Emily C. , Grubb Sarah R. , Warner Marcie H. , Montgomery Matthew T. , Garlena Rebecca A. , Russell Daniel A. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: August 2016

ABSTRACT

BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host
Gordonia terrae
3612. BetterKatz's genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced
Gordonia
phages.
Genome Sequences of
Gordonia
Phages Bowser and Schwabeltier
Authors: Montgomery Matthew T. , Pope Welkin H. , Arnold Zachary M. , Basina Aleksandra , Iyer Ankitha M. , Stoner Ty H. , Kasturiarachi Naomi S. , Pressimone Catherine A. , Schiebel Johnathon G. , Furbee Emily C. , Grubb Sarah R. , Warner Marcie H. , Garlena Rebecca A. , Russell Daniel A. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: August 2016

ABSTRACT

Gordonia
phages Bowser and Schwabeltier are newly isolated phages infecting
Gordonia terrae
3612. Bowser and Schwabeltier have similar siphoviral morphologies and their genomes are related to each other, but not to other phages. Their lysis cassettes are atypically situated among virion tail genes, and Bowser encodes two tyrosine integrases.
Genome Sequences of
Gordonia
Phages Hotorobo, Woes, and Monty
Authors: Pope Welkin H. , Davis Jameson P. , O'shea Sirinya , Pfeiffer Anastasia C. , Rich Alexandra N. , Xue Jason C. , Shedlock Kathleen A. , Stanton Ann-Catherine J. , Furbee Emily C. , Grubb Sarah R. , Warner Marcie H. , Montgomery Matthew T. , Garlena Rebecca A. , Russell Daniel A. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: August 2016

ABSTRACT

Hotorobo, Woes, and Monty are newly isolated bacteriophages of
Gordonia terrae
3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date.
Genome Sequences of
Gordonia
Phages BaxterFox, Kita, Nymphadora, and Yeezy
Authors: Pope Welkin H. , Bandla Sharanya , Colbert Alexandra K. , Eichinger Fiona G. , Gamburg Michelle B. , Horiates Stavroula G. , Jamison Jerrica M. , Julian Dana R. , Moore Whitney A. , Murthy Pranav , Powell Meghan C. , Smith Sydney V. , Mezghani Nadia , Milliken Katherine A. , Thompson Paige K. , Toner Chelsea L. , Ulbrich Megan C. , Furbee Emily C. , Grubb Sarah R. , Warner Marcie H. , Montgomery Matthew T. , Garlena Rebecca A. , Russell Daniel A. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: August 2016

ABSTRACT

Gordonia
phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of
Gordonia terrae
, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%.
Whole-Genome Sequence of
Corynebacterium auriscanis
Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom
Authors: Tiwari Sandeep , Jamal Syed Babar , Oliveira Leticia Castro , Clermont Dominique , Bizet Chantal , Mariano Diego , de Carvalho Paulo Vinicius Sanches Daltro , Souza Flavia , Pereira Felipe Luiz , de Castro Soares Siomar , Guimarães Luis C. , Dorella Fernanda , Carvalho Alex , Leal Carlos , Barh Debmalya , Figueiredo Henrique , Hassan Syed Shah , Azevedo Vasco , Silva Artur 
Published: August 2016

ABSTRACT

In this work, we describe a set of features of
Corynebacterium auriscanis
CIP 106629 and details of the draft genome sequence and annotation. The genome comprises a 2.5-Mbp-long single circular genome with 1,797 protein-coding genes, 5 rRNA, 50 tRNA, and 403 pseudogenes, with a G+C content of 58.50%.
Complete Genome Sequence of
Gluconacetobacter hansenii
Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose
Authors: Pfeffer Sarah , Mehta Kalpa , Brown R. Malcolm 
Published: August 2016

ABSTRACT

This study reports the release of the complete nucleotide sequence of
Gluconacetobacter hansenii
strain NQ5 (ATCC 53582). This strain was isolated by R. Malcolm Brown, Jr. in a sugar mill in North Queensland, Australia, and is an efficient producer of bacterial cellulose. The elucidation of the genome will contribute to the study of the molecular mechanisms necessary for cellulose biosynthesis.
Complete Genome Sequence of the Cyanobacterium
Anabaena
sp. 33047
Authors: Pfeffer Sarah , Brown R. Malcolm 
Published: August 2016

ABSTRACT

This study presents the complete nucleotide sequence of
Anabaena
sp. ATCC 33047 (
Anabaena
CA), a filamentous, nitrogen-fixing marine cyanobacterium, which under salt stress conditions accumulates sucrose internally. The elucidation of the genome will contribute to the understanding of cyanobacterial diversity.
Draft Genome Sequences of Two Magnetotactic Bacteria,
Magnetospirillum moscoviense
BB-1 and
Magnetospirillum marisnigri
SP-1
Authors: Koziaeva Veronika V. , Dziuba Marina V. , Ivanov Timophey M. , Kuznetsov Boris B. , Skryabin Konstantin G. , Grouzdev Denis S. 
Published: August 2016

ABSTRACT

We report here the draft genome sequences of two recently isolated magnetotactic species,
Magnetospirillum moscoviense
BB-1 and
Magnetospirillum marisnigri
SP-1. The genome of
M. moscoviense
BB-1 has 4,164,497 bp, 65.2% G+C content, and comprises 207 contigs. The genome of
M. marisnigri
SP-1 consists of 131 contigs and has a length of 4,619,819 bp and 64.7% G+C content.
Draft Genome Sequences of
Escherichia coli
Isolates from Wounded Military Personnel
Authors: Arivett Brock A. , Ream Dave C. , Fiester Steven E. , Kidane Destaalem , Actis Luis A. 
Published: August 2016

ABSTRACT

Members of the
Escherichia coli
bacterial family have been grouped as ESKAPE (
Enterococcus faecium
,
Staphylococcus aureus
,
Klebsiella pneumoniae
,
Acinetobacter baumannii
,
Pseudomonas aeruginosa
, and
Enterobacter
species) pathogens because of their extensive drug resistance phenotypes and increasing threat to human health. The genomes of six extended-spectrum β-lactamase (ESBL)-producing
E. coli
strains isolated from wounded military personnel were sequenced and annotated.
Draft Genome Sequences of
Pseudomonas aeruginosa
Isolates from Wounded Military Personnel
Authors: Arivett Brock A. , Ream Dave C. , Fiester Steven E. , Kidane Destaalem , Actis Luis A. 
Published: August 2016

ABSTRACT

Pseudomonas aeruginosa
, a Gram-negative bacterium that causes severe hospital-acquired infections, is grouped as an ESKAPE (
Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa
, and
Enterobacter
species) pathogen because of its extensive drug resistance phenotypes and effects on human health worldwide. Five multidrug resistant
P. aeruginosa
strains isolated from wounded military personnel were sequenced and annotated in this work.
Safety Recommendations for Moxa Use Based on the Concentration of Noxious Substances Produced during Commercial Indirect Moxibustion
Authors: Kwon O Sang , Cho Seong Jin , Choi Kwang-Ho , Yeon Sun Hee , Kang Suk-Yun , Kim Jae-hyo , Ahn Seong-Hun , Ryu Yeonhee 
Published: August 2016

Background Moxibustion therapy has been used historically for thousands of years and there are many clinical trials supporting its efficacy and effectiveness for various conditions. Moxa smoke has been a major reason for avoiding moxibustion due to its smell and potential risks to the human body. Methods 10 units of commercial indirect moxa (CIM) from six manufacturers (A–F) were burnt in a 2.5×2.5×2.5 m chamber without ventilation, and concentrations of carbon oxides (CO and CO2), nitrogen oxides (NOx), and volatile organic compounds (VOCs) from the indoor air samples were measured. Results For brands A, B, C, D, E, and F, respectively, relative to baseline values, we observed an increase in CO (from 0.002 to 0.007, 0.006, 0.005, 0.006, 0.005, and 0.006 parts per billion (ppb)), NOx (from 0.009 to 0.051, 0.025, 0.015, 0.050, 0.019, and 0.020 ppb), and total VOCs (TVOC; from 48.06 to 288.83, 227.93, 140.82, 223.22, 260.15, and 161.35 μg/m3), while the concentration of CO2 was not elevated. Each CIM brand demonstrated different VOC emission characteristics, which could be divided into three groups. On average, we estimated that 20 units of CIM or 2.41 g moxa floss would need to be combusted in order to exceed the safe levels set by Korean environmental law. This limit is likely to be greater in the case of a larger room or use of ventilation. Conclusions Despite increased CO/NOx/VOC concentrations, overall levels remained within safe limits. These findings may help clinicians to maintain safe moxibustion treatment conditions to help keep both patients and clinicians safe from the pollutants generated by moxa combustion.
Trends in diabetes in pregnancy in Sweden 1998–2012
Authors: Fadl Helena E , Simmons David 
Published: August 2016

ObjectiveDiabetes in pregnancy has been shown to increase in parallel with the increasing prevalence of obesity. In this national population-based study, we analyzed the trends for gestational diabetes mellitus (GDM), type 1 diabetes in pregnancy, and type 2 diabetes in pregnancy in Sweden between 1998 and 2012.Research design and methodsA population-based cohort study using the Swedish national medical birth registry data. The time periods were categorized into 3-year intervals and adjusted for maternal body mass index (BMI), ethnicity, and age in a logistic regression.ResultsEach type of diabetes increased over the studied 15-year period. Type 1 diabetes increased by 33.2% (22.2–45.3) and type 2 diabetes by 111% (62.2–174.4) in the adjusted model. Nordic women had the highest prevalence of type 1 diabetes (0·47%) compared with other ethnic groups. The increase in GDM and, to a lesser extent, type 2 diabetes was explained by country of birth, BMI, and maternal age. The prevalence of GDM in Nordic women (0.7–0.8%) did not increase significantly over the time period.ConclusionsAll types of diabetes in pregnancy increased over the 15-year time period in Sweden. Maternal pre-pregnancy BMI remains the key factor explaining the increase in GDM/type 2 diabetes. How to turn around the growing prevalence of diabetes in pregnancy, with its short-term and long-term health effects on both mother and child, requires population-based interventions that reduce the likelihood of entering pregnancy with a raised BMI.
How effective are brief interventions in reducing alcohol consumption: do the setting, practitioner group and content matter? Findings from a systematic review and metaregression analysis
Authors: Platt Lucy , Melendez-Torres G J , O'Donnell Amy , Bradley Jennifer , Newbury-Birch Dorothy , Kaner Eileen , Ashton Charlotte 
Published: August 2016

BackgroundWhile the efficacy and effectiveness of brief interventions for alcohol (ABI) have been demonstrated in primary care, there is weaker evidence in other settings and reviews do not consider differences in content. We conducted a systematic review to measure the effect of ABIs on alcohol consumption and how it differs by the setting, practitioner group and content of intervention.MethodsWe searched MEDLINE, EMBASE, PsycINFO; CINAHL, Social Science Citation Index, Cochrane Library and Global Health up to January 2015 for randomised controlled trials that measured effectiveness of ABIs on alcohol consumption. We grouped outcomes into measures of quantity and frequency indices. We used multilevel meta-analysis to estimate pooled effect sizes and tested for the effect of moderators through a multiparameter Wald test. Stratified analysis of a subset of quantity and frequency outcomes was conducted as a sensitivity check.Results52 trials were included contributing data on 29 891 individuals. ABIs reduced the quantity of alcohol consumed by 0.15 SDs. While neither the setting nor content appeared to significantly moderate intervention effectiveness, the provider did in some analyses. Interventions delivered by nurses had the most effect in reducing quantity (d=−0.23, 95% CI (−0.33 to −0.13)) but not frequency of alcohol consumption. All content groups had statistically significant mean effects, brief advice was the most effective in reducing quantity consumed (d=−0.20, 95% CI (−0.30 to −0.09)). Effects were maintained in the stratified sensitivity analysis at the first and last assessment time.ConclusionsABIs play a small but significant role in reducing alcohol consumption. Findings show the positive role of nurses in delivering interventions. The lack of evidence on the impact of content of intervention reinforces advice that services should select the ABI tool that best suits their needs.
Does pre-pregnancy BMI determine blood pressure during pregnancy? A prospective cohort study
Authors: Savitri Ary I , Zuithoff Peter , Browne Joyce L , Amelia Dwirani , Baharuddin Mohammad , Grobbee Diederick E , Uiterwaal Cuno S P M 
Published: August 2016

ObjectivesTo evaluate if pre-pregnancy body mass index (BMI) determines blood pressure throughout pregnancy and to explore the role of gestational weight gain in this association. In addition, the effects of pre-pregnancy BMI and gestational weight gain on the occurrence of gestational hypertension and pre-eclampsia were investigated.DesignProspective cohort study.SettingMaternal and child health primary care referral centre, Jakarta, Indonesia.Population and measurements2252 pregnant women visiting Budi Kemuliaan Hospital and its branch for regular antenatal care visits from July 2012 to April 2015. Pre-pregnancy BMI (kg/m2) was based on self-reported pre-pregnancy weight and measured height at first visit. Gestational weight gain was calculated as weight at the day of delivery minus the pre-pregnancy weight. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured during pregnancy at every visit. Linear mixed models were used to analyse this relation with repeated blood pressure measures as the outcome and pre-pregnancy BMI as the predictor. When looking at gestational hypertension and pre-eclampsia as outcomes, (multiple) logistic regression was used in the analysis.ResultsIndependent of pre-pregnancy BMI, SBP and DBP increased by 0.99 mm Hg/month and 0.46 mm Hg/month, respectively. Higher pre-pregnancy BMI was associated with higher pregnancy SBP (0.25 mm Hg/kg/m2; 95% CI 0.17 to 0.34; p<0.01) and DBP (0.18 mm Hg/kg/m2; 0.13 to 0.24; p<0.01) in adjusted analysis. Every 1 kg/m2higher pre-pregnancy BMI was associated with 6% and 9% higher odds for gestational hypertension (adjusted OR (aOR) 1.06; 95% CI 1.03 to 1.09; p<0.01) and pre-eclampsia (aOR 1.09; 1.04 to 1.14; p<0.01). Accounting for gestational weight gain did not attenuate these associations.ConclusionsPre-pregnancy BMI determines the level, but not the change, of blood pressure in pregnancy and is linked to higher odds for gestational hypertension and pre-eclampsia, independent of gestational weight gain.
Primary cervical cancer screening with an HPV mRNA test: a prospective cohort study
Authors: Sørbye Sveinung Wergeland , Fismen Silje , Gutteberg Tore Jarl , Mortensen Elin Synnøve , Skjeldestad Finn Egil 
Published: August 2016

ObjectivesTo assess the performance of a 5-type human papillomavirus (HPV) messenger RNA (mRNA) test in primary screening within the framework of the Norwegian population-based screening programme.DesignNationwide register-based cohort study.SettingIn 2003–2004, general practitioners and gynaecologists recruited 18 852 women for participation in a primary screening study with a 5-type HPV mRNA test.ParticipantsAfter excluding women with a history of abnormal smears and with cervical intraepithelial neoplasia grade 2 (CIN2+) before or until 3 months after screening, 11 220 women aged 25–69 years were eligible for study participation. The Norwegian Cancer Registry completed follow-up of CIN2+ through 31 December 2009.InterventionsFollow-up according to the algorithm for cytology outcomes in the population-based Norwegian Cervical Cancer Screening Programme.Main outcome measuresWe estimated cumulative incidence of CIN grade 3 or worse (CIN3+) 72 months after the 5-type HPV mRNA test.Results3.6% of the women were HPV mRNA-positive at baseline. The overall cumulative rate of CIN3+ was 1.3% (95% CI 1.1% to 1.5%) through 72 months of follow-up, 2.3% for women aged 25–33 years (n=3277) and 0.9% for women aged 34–69 years (n=7943). Cumulative CIN3+ rates by baseline status for HPV mRNA-positive and mRNA-negative women aged 25–33 years were 22.2% (95% CI 14.5% to 29.8%) and 0.9% (95% CI 0.4% to 1.4%), respectively, and 16.6% (95% CI 10.7% to 22.5%) and 0.5% (95% CI 0.4% to 0.7%), respectively, in women aged 34–69 years.ConclusionsThe present cumulative incidence of CIN3+ is similar to rates reported in screening studies via HPV DNA tests. Owing to differences in biological rationale and test characteristics, there is a trade-off between sensitivity and specificity that must be balanced when decisions on HPV tests in primary screening are taken. HPV mRNA testing may be used as primary screening for women aged 25–33 years and 34–69 years.
Improving the diagnostic quality and adequacy of shoulder radiographs in a District General Hospital
Authors: Richards Bethany , Riley James , Saithna Adnan 
Published: August 2016

A high rate of suboptimal shoulder radiographs was identified during a service evaluation exercise in our orthopaedic outpatient clinics. Inadequate radiographs require a return to the radiology department for further imaging, a resultant increased workload, delays in the clinic, increased radiation for patients, and inconvenience and decreased patient satisfaction. Furthermore, if a sub-optimal radiograph is accepted there is concern that diagnoses may be missed. The aim of this project was to decrease the rate of suboptimal radiographs by delivering a teaching package directed towards quality improvement.Evaluation criteria were set for standard orthopaedic shoulder radiographs (Anterior-posterior, axillary, and Velpeau views). Baseline data collection was performed over three, two-week periods and included all patients attending the shoulder clinic. The percentage of x-rays which were deemed adequate was only 19.4% for anterior-posterior views and 57.9% for axillary views.A comprehensive educational package was delivered to radiographers. This included a formal PowerPoint based teaching session, hands on training with practice using a skeleton, posters with step-by step instructions on how to obtain an adequate image, and PDF aide memoires suitable for viewing on a smartphone. Two subsequent two-week periods of data collection were performed to evaluate the benefit of this intervention.Delivery of focussed training and provision of easily accessible aide memoires to facilitate improved quality of radiographs resulted in a significant (p<0.05) reduction in the rate of inadequate images. There was also a significant decreases in the rate of return to the radiology department for repeat imaging.