bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing and functional validation of the JGI Brachypodium distachyon T‐DNA collection
Authors: Hsia Mon Mandy , O'Malley Ronan , Cartwright Amy , Nieu Rita , Gordon Sean P. , Kelly Sandra , Williams Tina G. , Wood Delilah F. , Zhao Yunjun , Bragg Jennifer , Jordan Mark , Pauly Markus , Ecker Joseph R. , Gu Yong , Vogel John P. 
Published: April 2017

SummaryDue to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T‐DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T‐DNA collection by 21 078, bringing the overall total to 26 112. Thirty‐seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T‐DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T‐DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.
Four decades of the morphological dynamics of the lakes in the Jianghan Plain using Landsat observations
Authors: Shi Yuming , Feng Lian , Gong Jianya 
Published: April 2017

AbstractUsing four decades of Landsat observations between 1978 and 2014, we documented and studied the long‐term dynamics of the inundation conditions in the Jianghan Plain, Central China. Three morphological factors, including inundation areas, perimeters and shoreline developments (SDs), of the 51 selected lakes were calculated. Significant long‐term morphological changes were found in lakes in the Jianghan Plain. The total area dramatically increased from 838.0 km2 in 1978 to 1200.8 km2 in 1989, and an overall decreasing trend was observed in the later period. The changing patterns of the perimeters and SDs were different from the inundation areas, especially for the largest lake in this area (Honghu). The inconsistent changes between the inundation area and the other two morphological parameters were likely caused by increasing human activities. This study demonstrated the importance of remote sensing in obtaining multi‐decadal lake changes in terms of both the inundation area and the morphological complexity.
An Evidence‐Based Approach to Reducing Cardiac Telemetry Alarm Fatigue
Authors: Srinivasa Ekta , Mankoo Jaspreet , Kerr Charles 
Published: April 2017

ABSTRACTBackgroundIt is estimated that between 80% and 99% of alarms in the clinical areas are in actionable alarms (Gross, Dahl, & Nielson). Alarm management is one of the Joint Commission's National Patient Safety Goals (2014) because sentinel events have directly been linked to the devices generating these alarms.PurposeAt an acute care facility in Boston, a multidisciplinary team consisting of Nursing, Biomedical Engineers, Patient Safety and Providers was formed to conduct a pilot study on the state of telemetry alarms on a surgical floor.MethodsAn evidence‐based approach was taken utilizing Philips Real‐time data exporter alarms tracking software to capture all telemetry alarms during a 43‐day time span. Likewise, noise meters were placed near telemetry alarm speakers to track decibel levels within the aforementioned timeframe for 21 days. Analysis of the data showed that clinically insignificant Premature Ventricular Contractions (PVC) alarms accounted for more than 40% of all alarms in the unit within the time span, while also contributing to an average noise level of 58.49 dB. In response to the data, the interdisciplinary team approved to permanently default the settings for PAIR PVC, MULTIFORM PVC, and RUN PVC alarms to off.ResultsThe results showed a 54% decrease in the rate of alarms per bed per day, and an average noise reduction of 2.3 dB between the two selected noise measurement areas.Linking Evidence to ActionOrganizing a multidisciplinary team provides an effective framework toward analyzing and addressing cardiac telemetry alarm fatigue. Looking at quantitative datasets for clinical care areas through various lenses helps identify opportunities for improvement in regards to highlighting alarms that are not actionable. Pilot changes to alarm parameters can be tested for their environmental impact in the care area.
Nurses’ Attitudes Toward the Single Checking of Medications
Authors: Cross Rachel , Bennett Paul N. , Ockerby Cherene , Wang Wei Chun , Currey Judy 
Published: April 2017

ABSTRACTBackground and AimThe policy of single over double checking of medications has been adopted by many health services; however, nurses’ attitudes toward single‐checking medications remains unclear. The aim of this study was to explore the attitudes of nurses who single check and administer medications in a setting where single checking has been in place for over a decade.MethodsA cross‐sectional survey design using the validated Single Checking Administration Medication Scale‐II to registered nurses (n = 299) working in one metropolitan teaching hospital in Victoria, Australia. Descriptive analyses for participants’ demographics were examined and confirmatory factor analysis (CFA) was performed on the survey items to represent the main themes of nurses’ attitudes toward single checking.ResultsNurses reported single checking allowed a greater accountability as a professional nurse and more control over drug administration. The efficiency of single checking was welcomed by nurses through reductions in administration time and workplace interruptions. Nurses were more likely to adhere to drug administration procedures when single checking and this process facilitated drug knowledge updates. There was significant variance in attitudes amongst nurses based upon current appointment and years of clinical experience. Free text responses indicated nurses’ attitudes were situated in the context of the traditional double‐checking system.Linking Evidence to ActionUnderstanding nurses’ attitudes toward single checking may assist health care services to positively address medication safety. Accountability, efficiency and knowledge are important for nurses when administering medications. Nurses’ attitudes are varied when correlated with demographic characteristics.
Diazotrophic Growth Allows Azotobacter vinelandii To Overcome the Deleterious Effects of a
glnE
Deletion
Authors: Mus Florence , Tseng Alex , Dixon Ray , Peters John W. 
Published: April 2017

ABSTRACT

Overcoming the inhibitory effects of excess environmental ammonium on nitrogenase synthesis or activity and preventing ammonium assimilation have been considered strategies to increase the amount of fixed nitrogen transferred from bacterial to plant partners in associative or symbiotic plant-diazotroph relationships. The GlnE adenylyltransferase/adenylyl-removing enzyme catalyzes reversible adenylylation of glutamine synthetase (GS), thereby affecting the posttranslational regulation of ammonium assimilation that is critical for the appropriate coordination of carbon and nitrogen assimilation. Since GS is key to the sole ammonium assimilation pathway of
Azotobacter vinelandii
, attempts to obtain deletion mutants in the gene encoding GS (
glnA
) have been unsuccessful. We have generated a
glnE
deletion strain, thus preventing posttranslational regulation of GS. The resultant strain containing constitutively active GS is unable to grow well on ammonium-containing medium, as previously observed in other organisms, and can be cultured only at low ammonium concentrations. This phenotype is caused by the lack of downregulation of GS activity, resulting in high intracellular glutamine levels and severe perturbation of the ratio of glutamine to 2-oxoglutarate under excess-nitrogen conditions. Interestingly, the mutant can grow diazotrophically at rates comparable to those of the wild type. This observation suggests that the control of nitrogen fixation-specific gene expression at the transcriptional level in response to 2-oxoglutarate via NifA is sufficiently tight to alone regulate ammonium production at levels appropriate for optimal carbon and nitrogen balance.

IMPORTANCE
In this study, the characterization of the
glnE
knockout mutant of the model diazotroph
Azotobacter vinelandii
provides significant insights into the integration of the regulatory mechanisms of ammonium production and ammonium assimilation during nitrogen fixation. The work reveals the profound fidelity of nitrogen fixation regulation in providing ammonium sufficient for maximal growth but constraining energetically costly excess production. A detailed fundamental understanding of the interplay between the regulation of ammonium production and assimilation is of paramount importance in exploiting existing and potentially engineering new plant-diazotroph relationships for improved agriculture.
Aerobic exercise promotes executive functions and impacts functional neural activity among older adults with vascular cognitive impairment
Authors: Hsu Chun Liang , Best John R , Davis Jennifer C , Nagamatsu Lindsay S , Wang Shirley , Boyd Lara A , Hsiung GY Robin , Voss Michelle W , Eng Janice Jennifer , Liu-Ambrose Teresa 
Published: April 2017

BackgroundVascular cognitive impairment (VCI) results from cerebrovascular disease, and worldwide, it is the second most common type of cognitive dysfunction. While targeted aerobic training is a promising approach to delay the progression of VCI by reducing cardiometabolic risk factors, few randomised controlled trials to date have specifically assessed the efficacy of aerobic training on cognitive and brain outcomes in this group at risk for functional decline.AimTo examine the effect of moderate-intensity aerobic training on executive functions and functional neural activity among older adults with mild subcortical ischaemic VCI (SIVCI).MethodsOlder adults with mild SIVCI were randomly assigned to: (1) 6-month, 3×/week aerobic training (n=10) or (2) usual care (control; n=11). Participants completed functional MRI (fMRI) at baseline and trial completion. During the fMRI sessions, behavioural performance on the Eriksen flanker task and task-evoked neural activity were assessed.ResultsAt trial completion, after adjusting for baseline general cognition, total white matter lesion volume and flanker performance, compared with the control group, the aerobic training group significantly improved flanker task reaction time. Moreover, compared with the controls, the aerobic training group demonstrated reduced activation in the left lateral occipital cortex and right superior temporal gyrus. Reduced activity in these brain regions was significantly associated with improved (ie, faster) flanker task performance at trial completion.SummaryAerobic training among older adults with mild SIVCI can improve executive functions and neural efficiency of associated brain areas. Future studies with greater sample size should be completed to replicate and extend these findings.
A realist review to explore how low-income pregnant women use food vouchers from the UK’s Healthy Start programme
Authors: Ohly Heather , Crossland Nicola , Dykes Fiona , Lowe Nicola , Hall-Moran Victoria 
Published: April 2017

ObjectivesTo explore how low-income pregnant women use Healthy Start food vouchers, the potential impacts of the programme, and which women might experience these impacts and why.DesignA realist review.Eligibility criteria for selecting studiesPrimary or empirical studies (of any design) were included if they contributed relevant evidence or insights about how low-income women use food vouchers from the Healthy Start (UK) or the Special Supplemental Nutrition Program for Women, Infants and Children (WIC) programmes. The assessment of ‘relevance’ was deliberately broad to ensure that reviewers remained open to new ideas from a variety of sources of evidence.AnalysisA combination of evidence synthesis and realist analysis techniques was used to modify, refine and substantiate programme theories, which were constructed as explanatory ‘context–mechanism–outcome’–configurations.Results38 primary studies were included in this review: four studies on Healthy Start and 34 studies on WIC. Two main outcome strands were identified: dietary improvements (intended) and financial assistance (unintended). Three evidence-informed programme theories were proposed to explain how aspects of context (and mechanisms) may generate these outcomes: the ‘relative value’ of healthy eating (prioritisation of resources); retailer discretion (pressure to ‘bend the rules’); the influence of other family members (disempowerment).ConclusionsThis realist review suggests that some low-income pregnant women may use Healthy Start vouchers to increase their consumption of fruits and vegetables and plain cow’s milk, whereas others may use them to reduce food expenditure and save money for other things.
Preparing future doctors for palliative care: views of course organisers
Authors: Walker Steven , Gibbins Jane , Paes Paul , Barclay Stephen , Adams Astrid , Chandratilake Madawa , Gishen Faye , Lodge Philip , Wee Bee 
Published: April 2017

BackgroundEffective training at medical school is essential to prepare new doctors to safely manage patients with palliative care (PC) and end of life care (EOLC) needs. The contribution of undergraduate PC course organisers is central but their collective views regarding role are unknown.ObjectiveTo survey attitudes of PC course organisers regarding their course, organisation, the adequacy of training provided and level of personal satisfaction.MethodsAn anonymised, multifactorial, web-based questionnaire was devised, tested, modified and then sent to lead PC course organisers at all UK medical schools.ResultsData were obtained from all 30 UK medical schools. Organisers agreed/strongly agreed (=agreed) that their PC course was highly rated by students (26, 87%). 25 (83%) agreed their course ‘enabled misconceptions and fears about PC, death, dying and bereavement to be addressed’, ‘delivered quality PC training’ (23, 77%), ‘fulfilled General Medical Council requirements’ (19, 63%), ‘prepared students well to care for patients with PC/EOLC needs’ (18, 60%) and ‘enabled students to visit a hospice and see the role of doctors in caring for the dying’ (17, 57%). Concerns were limited capacity to accommodate students (agreed 20, 66%) and variability in teaching according to location (15, 50%). Most agreed their institution recognised PC training as important (22, 73%), they felt supported by colleagues (21, 70%) and experienced cooperation between stakeholders (20, 67%). All agreed that PC training was essential for undergraduates, while 29 (97%) supported inclusion of a hospice visit in the curriculum. 27 agreed that their role was satisfying (90%), 3 disagreed (10%).ConclusionsApproximately two-thirds of organisers were generally positive about their PC course, institution and role. A minority expressed concerns; these may reflect suboptimal PC training at their medical school and poor preparation of new doctors.
Comparing two regimens of intravaginal misoprostol with intravaginal gemeprost for second-trimester pregnancy termination: a randomised controlled trial
Authors: Koh Daniel Seow Choon , Ang Esther Pei Jing , Coyuco Jurja Chua , Teo Hua Zhen , Huang Xiaoling , Wei Xing , Ng Mor Jack , Lim Serene Liqing , Tan Kok Hian 
Published: April 2017

AimTo compare the efficacy and safety of intravaginal misoprostol 200 µg, 400 µg and gemeprost regimens for second-trimester termination of pregnancy (TOP).MethodsA three- armed randomi sed controlled trial (Clinical Trial Certificate 1100015) where 116 women undergoing second-trimester TOP were given intravaginal misoprostol 200 µ g (n=37), misoprostol 400 µg (n=40) or gemeprost 1 mg (n=39) at 4- hour intervals until abortion occurred with a maximum of five doses.ResultsThe misoprostol 400 µg group had the highest incidence of successful abortions (92.5%) compared to the misoprostol 200 µg (70.3%;p=0.017) and gemeprost 1 mg (74.4%;p=0.037) within 48 hours. There was no significant difference in abortion rate between misoprostol 200 µg and gemeprost. The misoprostol 400 µg group had the highest incidence of fever (70.0%) compared to misoprostol 200 µg (24.3%;p<0.001) and gemeprost 1 mg (46.2%;p=0.041). The gemeprost group had the highest incidence of diarrhoea (38.5%) compared to misoprostol 400 µg (10.0%;p=0.004) and misoprostol 200 µg (8.1%;p=0.003) groups.ConclusionsIntravaginal misoprostol 400 µ g at 4- hour intervals was the most effective regimen but was associated with a high incidence of fever. Misoprostol 200 µg demonstrated similar effectiveness as gemeprost and had lower incidence of diarrhoea. Gemeprost should not be first line for medical therapy given the cost, storage requirements and lower efficacy.
A randomised controlled trial of a complex intervention to reduce children’s exposure to secondhand smoke in the home
Authors: Ratschen Elena , Thorley Rebecca , Jones Laura , Opazo Breton Magdalena , Cook Juliette , McNeill Ann , Britton John , Coleman Tim , Lewis Sarah 
Published: April 2017

ObjectivesExposing children to secondhand tobacco smoke (SHS) causes significant harm and occurs predominantly through smoking by caregivers in the family home. We report a trial of a complex intervention designed to reduce secondhand smoke exposure of children whose primary caregiver feels unable or unwilling to quit smoking.DesignAn open-label, parallel, randomised controlled trial.SettingDeprived communities in Nottingham City and County, EnglandParticipantsCaregivers resident in Nottingham City and County in England who were at least 18 years old, the main caregiver of a child aged under 5 years living in their household, and reported that they were smoking tobacco inside their home.InterventionsWe compared a complex intervention combining personalised feedback on home air quality, behavioural support and nicotine replacement therapy for temporary abstinence with usual care.Main outcomesThe primary outcome was change in air quality in the home, measured as average 16–24  hours levels of particulate matter of  < 2.5  µm diameter (PM2.5), between baseline and 12 weeks. Secondary outcomes included changes in maximum PM2.5, proportion of time PM2.5 exceeded WHO recommended levels of maximum exposure of 25  µg/mg3, child salivary cotinine, caregivers’ cigarette consumption, nicotine dependence, determination to stop smoking, quit attempts and quitting altogether during the intervention.ResultsArithmetic mean PM2.5 decreased significantly more (by 35.2 %; 95%  CI 12.7% to 51.9 %) in intervention than in usual care households, as did the proportion of time PM2.5 exceeded 25  µg/mg3, child salivary cotinine concentrations, caregivers’ cigarette consumption in the home, nicotine dependence, determination to quit and likelihood of having made a quit attempt.ConclusionsBy reducing exposure to SHS in the homes of children who live with smokers unable or unwilling to quit, this intervention offers huge potential to reduce children’s’ tobacco-related harm.Trial registration numberISRCTN81701383.This trial was funded by the UK National Institute for Health Research (NIHR): RP-PG-0608-10020
Simulation of subseismic joint and fault networks using a heuristic mechanical model
Authors: Gillespie Paul , Casini Giulio , Iben Hayley , O'Brien James F. 
Published: April 2017

Abstract
Flow simulations of fractured and faulted reservoirs require representation of subseismic structures about which subsurface data are limited. We describe a method for simulating fracture growth that is mechanically based but heuristic, allowing for realistic modelling of fracture networks with reasonable run times. The method takes a triangulated meshed surface as input, together with an initial stress field. Fractures initiate and grow based on the stress field, and the growing fractures relieve the stress in the mesh. We show that a wide range of bedding-plane joint networks can be modelled simply by varying the distribution and anisotropy of the initial stress field. The results are in good qualitative agreement with natural joint patterns. We then apply the method to a set of parallel veins and demonstrate how the variations in thickness of the veins can be represented. Lastly, we apply the method to the simulation of normal fault patterns on salt domes. We derive the stress field on the bedding surface using the horizon curvature. The modelled fault network shows both radial and concentric faults. The new method provides an effective means of modelling joint and fault networks that can be imported to the flow simulator.
Toll-like receptor 2 dominance over Toll-like receptor 4 in stressful conditions for its detrimental role in the heart
Authors: Bagchi Ashim K. , Akolkar Gauri , Mandal Soma , Ayyappan Prathapan , Yang Xi , Singal Pawan K. 
Published: April 2017

It has been suggested that Toll-like receptor (TLR)4 promotes IL-10-mediated cardiac cell survival, whereas another receptor, TLR2, from the same family, is detrimental. Here, we examined the interactive role of these two innate signaling molecules under stressful conditions, including IL-10 knockout (IL-10−/−) mice, global ischemia-reperfusion (I/R) injury in rat hearts, and in vitro short hairpin RNA experimental models in the presence or absence of IL-10 (10 ng/ml). Circulating and myocardial levels of TNF-α as well as apoptosis and fibrosis were higher in IL-10−/−mice. The increase in TLR2 in IL-10−/−hearts indicated its negative regulation by IL-10. Ex vivo I/R also caused a marked upregulation of TLR2 and TNF-α as well as apoptotic and fibrotic signals. However, a 40-min reperfusion with IL-10 triggered an increase in TLR4 expression and improved recovery of cardiac function. The increase in IL-1 receptor-associated kinase (IRAK)-M and IRAK-2 activity during I/R injury suggested their role in TLR2 signaling. In vitro inhibition of TLR4 activity as a consequence of RNA inhibition-mediated suppression of myeloid differentiation gene (MyD)88 suggested MyD88-dependent activation of TLR4. The inclusion of IL-10 during reperfusion also downregulated the expression of IRAK-2, TNF-α receptor-associated factor 1-interacting protein (TRAIP) and apoptotic signals, caspase-3, and the Bax-to-Bcl-xLratio. IL-10 reduced the TNF-α receptor-associated increase in TRAIP-induced apoptosis during I/R injury, which led to an increase in IL-1β to mitigate transforming growth factor-β receptor type I-mediated fibrosis. The IL-10 mitigation of these changes suggests that the stimulation through TLR4 signaling promotes IRAK-4 and phosphorylates IRAK-1 instead of IRAK-2 and may be an important therapeutic approach in restoring heart health in stress.NEW & NOTEWORTHY Under stress conditions such as downregulation of the IL-10 gene or ischemia-reperfusion injury, Toll-like receptor (TLR)4 and IL-1 receptor-associated kinase (IRAK)-1 activation is suppressed, along with the upregulation of TLR-2 and IRAK-2, resulting in fibrosis and apoptosis. It is suggested that IL-10 helps to maintain heart function during stress via myeloid differentiation gene 88/IRAK-4/IRAK-1-dependent TLR4 signaling.