bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of Varian TrueBeam electron phase–spaces for Monte Carlo simulation of MLC‐shaped fields
Authors: Lloyd Samantha A. M. , Gagne Isabelle M. , Bazalova‐Carter Magdalena , Zavgorodni Sergei 
Published: May 2016

Purpose:This work evaluates Varian's electron phase–space sources for Monte Carlo simulation of the TrueBeam for modulated electron radiation therapy (MERT) and combined, modulated photon and electron radiation therapy (MPERT) where fields are shaped by the photon multileaf collimator (MLC) and delivered at 70 cm SSD.Methods:Monte Carlo simulations performed with EGSnrc‐based BEAMnrc/DOSXYZnrc and penelope‐based PRIMO are compared against diode measurements for 5 × 5, 10 × 10, and 20 × 20 cm2 MLC‐shaped fields delivered with 6, 12, and 20 MeV electrons at 70 cm SSD (jaws set to 40 × 40 cm2). Depth dose curves and profiles are examined. In addition, EGSnrc‐based simulations of relative output as a function of MLC‐field size and jaw‐position are compared against ion chamber measurements for MLC‐shaped fields between 3 × 3 and 25 × 25 cm2 and jaw positions that range from the MLC‐field size to 40 × 40 cm2.Results:Percent depth dose curves generated by BEAMnrc/DOSXYZnrc and PRIMO agree with measurement within 2%, 2 mm except for PRIMO's 12 MeV, 20 × 20 cm2 field where 90% of dose points agree within 2%, 2 mm. Without the distance to agreement, differences between measurement and simulation are as large as 7.3%. Characterization of simulated dose parameters such as FWHM, penumbra width and depths of 90%, 80%, 50%, and 20% dose agree within 2 mm of measurement for all fields except for the FWHM of the 6 MeV, 20 × 20 cm2 field which falls within 2 mm distance to agreement. Differences between simulation and measurement exist in the profile shoulders and penumbra tails, in particular for 10 × 10 and 20 × 20 cm2 fields of 20 MeV electrons, where both sets of simulated data fall short of measurement by as much as 3.5%. BEAMnrc/DOSXYZnrc simulated outputs agree with measurement within 2.3% except for 6 MeV MLC‐shaped fields. Discrepancies here are as great as 5.5%.Conclusions:TrueBeam electron phase–spaces available from Varian have been implemented in two distinct Monte Carlo simulation packages to produce dose distributions and outputs that largely reflect measurement. Differences exist in the profile shoulders and penumbra tails for the 20 MeV phase–space off‐axis and in the outputs for the 6 MeV phase–space.
Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons
Authors: Laloi G. , Montarry J. , Guibert M. , Andrivon D. , Michot D. , Le May C. 
Published: May 2016

ABSTRACT

Ascochyta blight, caused by the necrotrophic ascomycete
Didymella pinodes
, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of
D. pinodes
, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520
D. pinodes
strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses.

IMPORTANCE
Ascochyta blight, caused by
Didymella pinodes
, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of
D. pinodes
, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic.
A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii
Authors: Lipscomb Gina L. , Conway Jonathan M. , Blumer-Schuette Sara E. , Kelly Robert M. , Adams Michael W. W. 
Published: May 2016

ABSTRACT

Caldicellulosiruptor bescii
, an anaerobic Gram-positive bacterium with an optimal growth temperature of 78°C, is the most thermophilic cellulose degrader known. It is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. Currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the
pyrF
genome region. The
pyrF
gene serves as a genetic marker to select for uracil prototrophy, and it can also be counterselected for loss via resistance to the compound 5-fluoroorotic acid (5-FOA). To expand the
C. bescii
genetic tool kit, kanamycin resistance was developed as a selection for genetic manipulation. A codon-optimized version of the highly thermostable kanamycin resistance gene (named Cb
htk
) allowed the use of kanamycin selection to obtain transformants of either replicating or integrating vector constructs in
C. bescii
. These strains showed resistance to kanamycin at concentrations >50 μg · ml
−1
, whereas wild-type
C. bescii
was sensitive to kanamycin at 10 μg · ml
−1
. In addition, placement of the Cb
htk
marker between homologous recombination regions in an integrating vector allowed direct selection of a chromosomal mutation using both kanamycin and 5-FOA. Furthermore, the use of kanamycin selection enabled the targeted deletion of the
pyrE
gene in wild-type
C. bescii
, generating a uracil auxotrophic genetic background strain resistant to 5-FOA. The
pyrE
gene functioned as a counterselectable marker, like
pyrF
, and was used together with Cb
htk
in the Δ
pyrE
background strain to delete genes encoding lactate dehydrogenase and the CbeI restriction enzyme.

IMPORTANCE
Caldicellulosiruptor bescii
is a thermophilic anaerobic bacterium with an optimal growth temperature of 78°C, and it has the ability to efficiently deconstruct nonpretreated lignocellulosic plant biomass. It is, therefore, of biotechnological interest for genetic engineering applications geared toward biofuel production. The current genetic system used with
C. bescii
is based upon only a single selection strategy, and this uses the gene involved in a primary biosynthetic pathway. There are many advantages with an additional genetic selection using an antibiotic. This presents a challenge for thermophilic microorganisms, as only a limited number of antibiotics are stable above 50°C, and a thermostable version of the enzyme conferring antibiotic resistance must be obtained. In this work, we have developed a selection system for
C. bescii
using the antibiotic kanamycin and have shown that, in combination with the biosynthetic gene marker, it can be used to efficiently delete genes in this organism.
Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches
Authors: Ahmed W. , Hamilton K. A. , Gyawali P. , Toze S. , Haas C. N. 
Published: May 2016

ABSTRACT

Avian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (
n
= 20) and a range of nonpossum hosts (
n
= 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 10
7
gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 10
5
gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613–622, 2016,
http://dx.doi.org/10.1016/j.watres.2015.10.050
). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (
n
= 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 10
2
to 8.5 × 10
5
gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 10
3
to 6.8 × 10
3
gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use.

IMPORTANCE
The use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces.
Different Cellular Origins and Functions of Extracellular Proteins from Escherichia coli O157:H7 and O104:H4 as Determined by Comparative Proteomic Analysis
Authors: Islam Nazrul , Nagy Attila , Garrett Wesley M. , Shelton Dan , Cooper Bret , Nou Xiangwu 
Published: May 2016

ABSTRACT

Extracellular proteins play important roles in bacterial interactions with the environmental matrices. In this study, we examined the extracellular proteins from
Escherichia coli
O157:H7 and O104:H4 by tandem mass spectrometry. We identified 500 and 859 proteins from the growth media of
E. coli
O157:H7 and O104:H4, respectively, including 371 proteins common to both strains. Among proteins that were considered specific to
E. coli
O157:H7 or present at higher relative abundances in O157:H7 medium, most (57 of 65) had secretion signal sequences in their encoding genes. Noticeably, the proteins included locus of enterocyte effacement (LEE) virulence factors, proteins required for peptidyl-lipoprotein accumulation, and proteins involved in iron scavenging. In contrast, a much smaller proportion of proteins (37 of 150) that were considered specific to O104:H4 or presented at higher relative abundances in O104:H4 medium had signals targeting them for secretion. These proteins included Shiga toxin 2 subunit B and O104:H4 signature proteins, including AAF/1 major fimbrial subunit and serine protease autotransporters. Most of the abundant proteins from the growth medium of
E. coli
O104:H4 were annotated as having functions in the cytoplasm. We provide evidence that the extensive presence of cytoplasmic proteins in
E. coli
O104:H4 growth medium was due to biological processes independent of cell lysis, indicating alternative mechanisms for this potent pathogen releasing cytoplasmic contents into the growth milieu, which could play a role in interaction with the environmental matrices, such as pathogenesis and biofilm formation.

IMPORTANCE
In this study, we compared the extracellular proteins from two of the most prominent foodborne pathogenic
E. coli
organisms that have caused severe outbreaks in the United States and in Europe.
E. coli
O157:H7 is a well-studied Shiga toxigenic foodborne pathogen of the enterohemorrhagic pathotype that has caused numerous outbreaks associated with various contaminated foods worldwide.
E. coli
O104:H4 is a newly emerged Shiga toxigenic foodborne pathogen of the enteroaggregative pathotype that gained notoriety for causing one of the most deadly foodborne outbreaks in Europe in 2011. Comparison of proteins in the growth medium revealed significant differences in the compositions of the extracellular proteins for these two pathogens. These differences may provide valuable information regarding the cellular responses of these pathogens to their environment, including cell survival and pathogenesis.
Impact of exercise selection on hamstring muscle activation
Authors: Bourne Matthew N , Williams Morgan D , Opar David A , Al Najjar Aiman , Kerr Graham K , Shield Anthony J 
Published: May 2016

ObjectiveTo determine which strength training exercises selectively activate the biceps femoris long head (BFLongHead) muscle.MethodsWe recruited 24 recreationally active men for this two-part observational study.Part 1: We explored the amplitudes and the ratios of lateral (BF) to medial hamstring (MH) normalised electromyography (nEMG) during the concentric and eccentric phases of 10 common strength training exercises. Part 2: We used functional MRI (fMRI) to determine the spatial patterns of hamstring activation during two exercises which (1) most selectively and (2) least selectively activated the BF in part 1.ResultsEccentrically, the largest BF/MH nEMG ratio occurred in the 45° hip-extension exercise; the lowest was in the Nordic hamstring (Nordic) and bent-knee bridge exercises. Concentrically, the highest BF/MH nEMG ratio occurred during the lunge and 45° hip extension; the lowest was during the leg curl and bent-knee bridge. fMRI revealed a greater BF(LongHead)to semitendinosus activation ratio in the 45° hip extension than the Nordic (p<0.001). The T2 increase after hip extension for BFLongHead, semitendinosus and semimembranosus muscles was greater than that for BFShortHead(p<0.001). During the Nordic, the T2 increase was greater for the semitendinosus than for the other hamstring muscles (p≤0.002).SummaryWe highlight the heterogeneity of hamstring activation patterns in different tasks. Hip-extension exercise selectively activates the long hamstrings, and the Nordic exercise preferentially recruits the semitendinosus. These findings have implications for strategies to prevent hamstring injury as well as potentially for clinicians targeting specific hamstring components for treatment (mechanotherapy).
Strengthening leadership as a catalyst for enhanced patient safety culture: a repeated cross-sectional experimental study
Authors: Kristensen Solvejg , Christensen Karl Bang , Jaquet Annette , Møller Beck Carsten , Sabroe Svend , Bartels Paul , Mainz Jan 
Published: May 2016

ObjectivesCurrent literature emphasises that clinical leaders are in a position to enable a culture of safety, and that the safety culture is a performance mediator with the potential to influence patient outcomes. This paper aims to investigate staff's perceptions of patient safety culture in a Danish psychiatric department before and after a leadership intervention.MethodsA repeated cross-sectional experimental study by design was applied. In 2 surveys, healthcare staff were asked about their perceptions of the patient safety culture using the 7 patient safety culture dimensions in the Safety Attitudes Questionnaire. To broaden knowledge and strengthen leadership skills, a multicomponent programme consisting of academic input, exercises, reflections and discussions, networking, and action learning was implemented among the clinical area level leaders.ResultsIn total, 358 and 325 staff members participated before and after the intervention, respectively. 19 of the staff members were clinical area level leaders. In both surveys, the response rate was >75%. The proportion of frontline staff with positive attitudes improved by ≥5% for 5 of the 7 patient safety culture dimensions over time. 6 patient safety culture dimensions became more positive (increase in mean) (p<0.05). Frontline staff became more positive on all dimensions except stress recognition (p<0.05). For the leaders, the opposite was the case (p<0.05). Staff leaving the department after the first measurement had rated job satisfaction lower than the staff staying on (p<0.05).ConclusionsThe improvements documented in the patient safety culture are remarkable, and imply that strengthening the leadership can act as a significant catalyst for patient safety culture improvement. Further studies using a longitudinal study design are recommended to investigate the mechanism behind leadership's influence on patient safety culture, sustainability of improvements over time, and the association of change in the patient safety culture measures with change in psychiatric patient safety outcomes.
Prescribed opioids in primary care: cross-sectional and longitudinal analyses of influence of patient and practice characteristics
Authors: Foy Robbie , Leaman Ben , McCrorie Carolyn , Petty Duncan , House Allan , Bennett Michael , Carder Paul , Faulkner Simon , Glidewell Liz , West Robert 
Published: May 2016

ObjectivesTo examine trends in opioid prescribing in primary care, identify patient and general practice characteristics associated with long-term and stronger opioid prescribing, and identify associations with changes in opioid prescribing.DesignTrend, cross-sectional and longitudinal analyses of routinely recorded patient data.Setting111 primary care practices in Leeds and Bradford, UK.ParticipantsWe observed 471 828 patient-years in which all patients represented had at least 1 opioid prescription between April 2005 and March 2012. A cross-sectional analysis included 99 847 patients prescribed opioids between April 2011 and March 2012. A longitudinal analysis included 49 065 patient-years between April 2008 and March 2012. We excluded patients with cancer or treated for substance misuse.Main outcome measuresLong-term opioid prescribing (4 or more prescriptions within 12 months), stronger opioid prescribing and stepping up to or down from stronger opioids.ResultsOpioid prescribing in the adult population almost doubled for weaker opioids over 2005–2012 and rose over sixfold for stronger opioids. There was marked variation among general practices in the odds of patients stepping up to stronger opioids compared with those not stepping up (range 0.31–3.36), unexplained by practice-level variables. Stepping up to stronger opioids was most strongly associated with being underweight (adjusted OR 3.26, 1.49 to 7.17), increasing polypharmacy (4.15, 3.26 to 5.29 for 10 or more repeat prescriptions), increasing numbers of primary care appointments (3.04, 2.48 to 3.73 for over 12 appointments in the year) and referrals to specialist pain services (5.17, 4.37 to 6.12). Compared with women under 50 years, men under 50 were less likely to step down once prescribed stronger opioids (0.53, 0.37 to 0.75).ConclusionsWhile clinicians should be alert to patients at risk of escalated opioid prescribing, much prescribing variation may be attributable to clinical behaviour. Effective strategies targeting clinicians and patients are needed to curb rising prescribing, especially of stronger opioids.
Exploring the views of GPs, people with dementia and their carers on assistive technology: a qualitative study
Authors: Newton Lisa , Dickinson Claire , Gibson Grant , Brittain Katie , Robinson Louise 
Published: May 2016

ObjectivesTo explore the views and experiences of people with dementia, their family carers and general practitioners (GPs) on their knowledge and experience of accessing information about, and use of, assistive technology (AT) in dementia care.DesignQualitative methods with semistructured interviews and thematic analysis.Participants56 participants comprising 17 GPs, 13 people with dementia and 26 family carers.SettingCommunity care settings in the North East of England.Results4 main themes emerged: awareness and experience of AT; accessing information on AT; roles and responsibilities in the current care system and the future commissioning of AT services. All participants had practical experience of witnessing AT being used in practice. For people with dementia and their families, knowledge was usually gained from personal experience rather than from health and social care professionals. For GPs, knowledge was largely gained through experiential, patient-led learning. All groups acknowledged the important role of the voluntary sector but agreed a need for clear information pathways for AT; such pathways were perceived to be essential to both service providers and service commissioners.ConclusionsPeople with dementia and their family carers appear to be mainly responsible for driving a gradual increase in both awareness and the use of AT in dementia care. GPs should be equipped with the relevant knowledge to ensure families living with dementia receive appropriate information and support to enable them to live independently for as long as possible. There is an urgent need to simplify current complex community care pathways; as demonstrated in other chronic health conditions, a single point of access and a named lead professional may improve future care.
Pregnancy outcomes in Lebanese women with multiple sclerosis (the LeMS study): a prospective multicentre study
Authors: Fares Jawad , Nassar Anwar H , Gebeily Souheil , Kobeissy Firas , Fares Youssef 
Published: May 2016

ObjectiveThe Lebanese Multiple Sclerosis (LeMS) study aims to assess the influence of pregnancy and delivery on the clinical course of multiple sclerosis (MS) in Lebanese women.SettingThis prospective multicentre study took place in three MS referral university medical centres in Lebanon.ParticipantsIncluded were 29 women over 18 years who had been diagnosed with MS according to the McDonald criteria, and became pregnant between 1995 and 2015. Participating women should have stopped treatment 3 months before conception and become pregnant after the onset of MS. Women were followed up from 1 year preconceptionally and for 4 years postpartum.Main outcome measuresThe annualised relapse rates per participant during each 3-month period during pregnancy and each year postpartum were compared with the relapse rate during the year before pregnancy using the paired two-tailed t test. p Values <0.05 were considered statistically significant for all analyses (95% CI).Results64 full-term pregnancies were recorded. All pregnancies (100%) resulted in live births, with no complications or other diseases. In comparison with the prepregnancy year, in which the mean relapse rate±SE was 0.17±0.07, there was a significant reduction in the relapse rate during pregnancy and in the first year postpartum (p=0.02), but an increase in the rate in the second year postpartum (0.21±0.08). Thereafter, from the third year postpartum through the following fourth year, the annualised relapse rate fell slightly but did not differ from the annualised relapse rate recorded in the prepregnancy year (0.17±0.07).ConclusionsPregnancy in Lebanese women with MS does not seem to increase the risk of complications. No relapses were observed during pregnancy and in the first year postpartum; however, relapses rebounded in the second year postpartum, and over the long term, returned to the levels that preceded pregnancy.