bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil
Authors: Kim Seong-Jae , Kweon Ohgew , Sutherland John B. , Kim Hyun-Lee , Jones Richard C. , Burback Brian L. , Graves Steven W. , Psurny Edward , Cerniglia Carl E. 
Published: April 2015

ABSTRACT

We investigated the response of the hydrocarbon-degrading
Mycobacterium vanbaalenii
PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses.
M. vanbaalenii
PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C
12
and C
13
being degraded at the highest rate, although alkanes up to C
28
were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up- and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of
M. vanbaalenii
PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.
Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems
Authors: Yan Yan , Kuramae Eiko E. , Klinkhamer Peter G. L. , van Veen Johannes A. 
Published: April 2015

ABSTRACT

It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with
Proteobacteria
as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with
Proteobacteria
,
Bacteroidetes
, and
Verrucomicrobia
as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.
Quitting experiences and preferences for a future quit attempt: a study among inpatient smokers
Authors: Thomas Dennis , Abramson Michael J , Bonevski Billie , Taylor Simone , Poole Susan G , Weeks Gregory R , Dooley Michael J , George Johnson 
Published: April 2015

ObjectiveUnderstanding smokers’ quit experiences and their preferences for a future quit attempt may aid in the development of effective cessation treatments. The aims of this study were to measure tobacco use behaviour; previous quit attempts and outcomes; methods used to assist quitting; difficulties experienced during previous attempts; the motives and preferred methods to assist quitting in a future attempt; identify the factors associated with preferences for smoking cessation.DesignFace-to-face interview using a structured questionnaire.SettingInpatient wards of three Australian public hospitals.ParticipantsHospitalised smokers enrolled in a smoking cessation trial.ResultsOf 600 enrolled patients (42.8% participation rate), 64.3% (n=386) had attempted quitting in the previous 12 months. On a scale of 1 (low) to 10 (high), current motivation to quit smoking was high (median 9; IQR 6.5–10), but confidence was modest (median 5; IQR 3–8). Among 386 participants who reported past quit attempts, 69.9% (n=270) had used at least one cessation aid to assist quitting. Nicotine replacement therapy (NRT) was most commonly stated (222, 57.5%), although the majority had used NRT for <4 weeks. Hypnotherapy was the most common (68, 17.6%) non-pharmacological treatment. Over 80% (n=311) experienced withdrawal symptoms; craving and irritability were commonly reported. Most participants (351, 58.5%) believed medications, especially NRT (322, 53.7%), would assist them to quit in the future. History of previous smoking cessation medication use was the only independent predictor of interest in using medications for a future quit attempt.ConclusionsThe majority of smokers had attempted quitting in the previous 12 months; NRT was a popular cessation treatment, although it was not used as recommended by most. This suggests a need for assistance in the selection and optimal use of cessation aids for hospitalised smokers.Trial registration numberAustralian and New Zealand Clinical Trials Registry: ACTRN12612000368831.
One-step extrapolation of the prediction performance of a gene signature derived from a small study
Authors: Wang Ling-Yi , Lee Wen-Chung 
Published: April 2015

ObjectiveMicroarray-related studies often involve a very large number of genes and small sample size. Cross-validating or bootstrapping is therefore imperative to obtain a fair assessment of the prediction/classification performance of a gene signature. A deficiency of these methods is the reduced training sample size because of the partition process in cross-validation and sampling with replacement in bootstrapping. To address this problem, we aim to obtain a prediction performance estimate that strikes a good balance between bias and variance and has a small root mean squared error.MethodsWe propose to make a one-step extrapolation from the fitted learning curve to estimate the prediction/classification performance of the model trained by all the samples.ResultsSimulation studies show that the method strikes a good balance between bias and variance and has a small root mean squared error. Three microarray data sets are used for demonstration.ConclusionsOur method is advocated to estimate the prediction performance of a gene signature derived from a small study.
DO PARAMEDICS FIND IT BENEFICIAL TO LEARN THE DIAGNOSIS GIVEN TO THEIR PATIENTS IN THE EMERGENCY DEPARTMENT?
Authors: Pollard John , Black Sarah 
Published: April 2015

BackgroundTraditionally, paramedics do not learn the diagnosis of a patient once handed over at the Emergency Department (ED). In this pilot study, a system of feedback from the ED was provided to a group of paramedics using secure email. The diagnosis given in ED and discharge destination of their patients was provided in an anonymised format.MethodsAfter receiving the feedback for eight weeks a questionnaire was distributed electronically to participating paramedics. The survey aimed to establish the perceived usefulness of the feedback by asking a series of questions with dichotomous response options. The facility to elaborate on some responses was also provided.ResultsA 76% response rate was achieved with 19 of the 25 clinicians who received the feedback report returning the survey. Of those who responded 90% (n=17) indicated that it prompted them to reflect clinically, with 65% (n=11) noting that this included further reading. Some said the reading included key texts and guidelines to refresh knowledge, while others read around a specific subject to broaden their knowledge. 68% (n=13) indicated that the feedback had prompted clinical discussion with colleagues. A key question asked respondents if the ED diagnosis differed from their pre-hospital clinical impression, 63% (n=12) noted that there was a difference. Unanimously respondents thought receiving the feedback reports would help improve their skill in diagnosis and wanted to continue receiving them.Limiting factorsThis was a convenience sample of small size. Receiving feedback on the diagnosis given in ED is a novel experience for paramedics.ConclusionsReceiving this feedback enables paramedics to audit the quality of their work. They find this beneficial and there is the potential to improve skill in diagnosis. Further studies in this area are suggested.
EMERGENCY MEDICAL DISPATCH: DO THE DEAD TAKE PRIORITY OVER THE DYING?
Authors: Hitt Andy , Williams Julia , Edwards Tim 
Published: April 2015

BackgroundIn the UK demand for emergency ambulances is increasing. To deal with this increase, Ambulance Service Trusts must use resources effectively and ensure that they are deployed appropriately.AimThe aim of this study was to gain an understanding of factors influencing resource dispatchers' (RD) decision-making processes when managing ambulance resources attending out-of-hospital cardiac arrest (OOHCA) and how these decisions might impact on resource availability.MethodUtilising a generic qualitative approach, nine RDs participated in semi structured interviews which were recorded and transcribed verbatim. Data analysis was performed using a template style of thematic analysis.FindingsOOHCA generally takes priority over other emergency calls regardless of clinical need or likely prognosis. Participants stated that they would probably drive past a critically ill patient to attend a patient in cardiac arrest even if they believed them to be beyond help. A significant amount of time was spent dealing with deceased patients, especially when waiting for police to attend. This may affect resource availability and subsequently delay treatment of other critically ill and injured patients.LimitationsDispatching processes may differ between Trusts so further studies are required to enhance transferability of findings.ConclusionsOOHCA is almost always prioritised above other time critical emergencies despite the view that other patients may benefit more from a priority response. Decisions are made rapidly, under pressure and with very little clinical information to hand.Recommendations for changeFurther research is required before substantive recommendations can be made but preliminary indications infer that resource efficiency may be improved by applying simple changes to every day practice including dialogue between lead clinician and dispatcher to optimise staff skill mix in attendance to calls and improved liaison between police and ambulance controls to facilitate the prompt stand down of ambulance resources dealing with deceased patients.
USING POINT-OF-CARE CARDIAC MARKERS IN LOW RISK CHEST PAIN IN THE EMERGENCY DEPARTMENT
Authors: Griffiths James , Humphrey Julian , Pearson Sally-Anne , Pallot David 
Published: April 2015

BackgroundBarnsley Emergency Department, which recruited patients into the RATPAC trial, initiated a POC pathway for low-risk chest pain patients from December 2011. A preceding audit estimated that 50% of chest pain patients may be suitable for discharge from the ED.MethodsAll patients who underwent POC testing for chest pain between December 2011 and July 2012 were identified from the Radiometer AQT™ database. Patient notes were then examined using Filestream™ data record system and time spent within the ED was assessed using Extramed™ patient tracking system.ResultsA total of 1039 patients underwent POC testing during the period. Of these, 9 sets of notes were missing, giving a sample of 1030 patients. The age range was 16–96 (mean age 53.7 years) and 553 (54%) patients were male.Admissions: 649 patients were discharged from the ED (63%). However, when high risk patients and those admitted for other reasons (different diagnosis or social reasons), this percentage rises to 83% (649 discharges from 784 appropriate POC patients).Re-attendances: There were a total of 137 re-attendances within one month (13% of all patients). When unrelated attendances are removed, the number of significant re-attendances was 43 (4% of patients).Breaches: There were a total of 120 patients (11.6%) who breached the 4-hour access standard. During the 8-month period, there were a total of 2147 breaches and the average 4-hour performance for the trust was 95.65%. For the same period in the previous year, there were 2779 breaches and the average 4-hour performance was 94.27%ConclusionOur pilot work would suggest that the use of POC cardiac markers in chest pain can facilitate discharge of low risk patients from the Emergency Department without a significant re-attendance rate or impacting on the 4-hour access standard.
WHERE NEXT FOR THE PARAMEDIC PROFESSION? AN ETHNOGRAPHY OF WORK CULTURE AND OCCUPATIONAL IDENTITY
Authors: McCann Leo , Granter Edward , Hassard John , Hyde Paula 
Published: April 2015

The paramedic profession, along with the broader structure and mission of NHS emergency ambulance provision, is undergoing significant but rather undefined change. The clinical scope of the paramedic role has broadened, and the opening of new patient pathways has enabled a broader range of treatment and referral options for attending ambulance crews.Ambulance trusts have moved to an all-graduate intake for new paramedics, and significant advances have been made in establishing the classic steps of a ‘professionalization project’ (such as the growth of the College of Paramedics, the development of peer-reviewed practitioner journals, and the introduction of advanced paramedic roles.) Some of these changes are contentious, however, and many of the fundamentals of ambulance work and occupational culture remain unchanged to a significant degree.Long-standing problems persist around low staff morale, high levels of sickness-related absence, lack of capacity, limited resources and support, the dominance of a ‘targets culture’, and a lack of working trust between ‘management’ and ‘roadstaff.’ Working life ‘on the road’ is demanding and the emergency ambulance field is a challenging environment for the pursuit of a professionalization project.This paper provides insights from a sociology of work perspective into the everyday work culture of ambulance services. Based on qualitative interviews and ethnographic observation of ambulance crews and of mid-level ambulance trust managers, the paper provides an in-depth exploration of the culture of everyday working life in (anonymized) ambulance trusts.We identify several broad conceptions among staff as to the essence and purpose of emergency ambulance provision, of ambulance trusts as employers, and of the goals and potential pitfalls of the professionalization project. The paper thus explores the multifaceted meanings of ‘professionalism’ and considers the broad challenges facing the profession at large and NHS trusts as employers as both confront unsettling forms of change.
WHAT CLINICAL REASONING STRATEGIES DO STUDENT PARAMEDICS USE DURING THEIR DIFFERENTIATION OF PATIENTS WITH DIFFICULTY IN BREATHING?
Authors: Catterall M , Williams J 
Published: April 2015

BackgroundAcute heart failure (AHF) symptoms are similar to some respiratory conditions making it challenging for paramedics to diagnose AHF accurately, especially as they infrequently encounter it. Little is known about the clinical reasoning strategies (CRS) used by student or qualified paramedics to diagnose and manage patients with AHF, inaccurate diagnosis associated with inappropriate diuretic management can cause patient complications.Research aimTo explore CRS student paramedics use during their diagnosis and management of AHF, examining differentiation processes between AHF and a respiratory condition presenting with similar signs and symptoms.MethodologyA convenience sample of ten senior student paramedics from a BSc (Hons) Paramedic Science programme participated in a two phase exploratory study. Phase A involved assessment of three high-fidelity simulations of: (a) AHF; (b) pneumonia; (c) infective exacerbation of chronic obstructive pulmonary disease each patient complaining of breathlessness. Phase B incorporated semi-structured interviews to explore participants' CRS during these simulations. Data analysis used thematic analysis.Findings and discussionFour key themes emerged: (i) Identification of Heart Failure; (ii) Process of Differentiation; (iii) Sources of Influence; (iv) Management Decisions. Participants demonstrated two forms of CRS; initially backward reasoning, using illness-scripts, rapidly determined need for immediate resuscitation and evaluated the opportunity available to conduct assessment and examination. This involved searching for cues used in forward hypothetical-deductive clinical reasoning; the strategy participants used during diagnosis. Two participants inappropriately activated illness-scripts through cue misinterpretation, resulting in incorrect diagnosis and pharmacological therapy. Participants had a low-threshold of pharmacological treatment instigation, even when the diagnosis was uncertain.ConclusionAlthough a small study, consideration should be given to participants immature CRS; they may require post-registration support to develop consistently accurate and appropriate clinical decisions which avoid patient exposure to risk. Further research should identify whether other paramedic students, from the various registration routes, reflect these results.
WHAT DO USERS VALUE ABOUT THE EMERGENCY AMBULANCE SERVICE?
Authors: Togher Fiona , Turner Janette , Siriwardena Aloysius Niroshan , O'Cathain Alicia 
Published: April 2015

IntroductionResponse times have been used as a key quality indicator for emergency ambulance services in the United Kingdom, but criticised for their narrow focus. Consequently, there is a need to consider wider measures of quality. The patient perspective is becoming an increasingly important dimension in pre-hospital outcomes research. To that end, we aimed to investigate patients' experiences of the 999 ambulance service to understand the processes and outcomes important to them.MethodsWe employed a qualitative design, using semi-structured interviews with a purposive sample of people who had recently used a 999 ambulance in the East Midlands. We recruited patients of different age, sex, geographical location, and ambulance service response including ‘hear and treat’, ‘see and treat’ and ‘see and convey’.ResultsWe interviewed 20 service users. Eleven men and nine women participated and 12 were aged 65 years and over. Users valued a quick response when they perceived the call to be an emergency. This was of less value to those who did not perceive their situation as an emergency and irrelevant to ‘hear and treat’ users. All users valued the professional approach and information and advice given by call handlers, crew and first responders, which provided them with reassurance in a worrying situation. ‘See and convey’ users valued a seamless handover to secondary care.LimitationsWe found it challenging to engage participants to consider quality indicators beyond response times because these were considered to be abstract in comparison with their concrete experiences.Conclusions and recommendationsAspects other than response times were important to patients, particularly in situations perceived by patients to be non-emergency. The results will be combined with issues identified from systematic reviews and used in a Delphi study to identify candidates for new outcome measures for emergency ambulance services.
DEVELOPMENT OF COMPLEX INTERVENTION IN EMERGENCY CARE OF FALLS FOR EVALUATION:IMPLEMENTATION OF THE MRC GUIDANCE
Authors: Chatters R , Mason S , Snooks H ,   The SAFER 2 team
Published: April 2015

BackgroundThe Medical Research Council (MRC) guidance for the development and evaluation of complex interventions describes such an intervention as one which has several interacting components; the MRC recommends that complex interventions are developed through literature identification, modelling of processes and theory development. We describe the utilisation of this guidance to develop the SAFER 2 (Support and Assessment for Fall Emergency Referrals) study intervention—a multi-centre randomised controlled trial (RCT) looking to improve the care Ambulance Services provide to elderly patients who fall.MethodsLiterature was identified using MedLine and through applicant's previous work in this field. Two pilot studies were undertaken in two UK ambulance services; an economic evaluation was identified. A workshop, incorporating stakeholders from ambulance services, acute trusts and primary care, allowed further development and finalisation of the intervention. Specialist sub-groups were set-up to develop specific components of the interventionResultsLiterature review identified previous RCTs and a recent systematic review, highlighting the need for a comprehensive evaluation of the ability of paramedics to safely make decisions to not convey elderly patients who fall to hospital and the effect of direct referral to multi-factorial community interventions on such patients. Pilot studies reinforced the need for an intervention that improves paramedic's decision making. The workshop resulted in the amalgamation of all evidence and agreement of the final intervention by all stakeholders.The final definition of the intervention comprised of paramedic training, patient assessment tool, referral tool, process of referral, clinical support and Falls Prevention Service make-up and response.DiscussionThorough intervention development and effective implementation are vital to the success of SAFER 2 and other studies in this field. In order to produce generalisable evidence about clinical and cost effectiveness that is reproducible, the intervention needs to be clearly defined with input and agreement from study stakeholders.