bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete 4.55-Megabase-Pair Genome of “
Candidatus
Fluviicola riflensis,” Curated from Short-Read Metagenomic Sequences
Authors: Banfield Jillian F. , Anantharaman Karthik , Williams Kenneth H. , Thomas Brian C. 
Published: November 2017

ABSTRACT

We report the 4.55-Mbp genome of “
Candidatus
Fluviicola riflensis” (
Bacteroidetes
) that was manually curated to completion from Illumina data. “
Ca
. Fluviicola riflensis” is a facultative anaerobe. Its ability to grow over a range of O
2
levels may favor its proliferation in an aquifer adjacent to the Colorado River in the United States.
Complete Genome Sequence of Human Coronavirus Strain 229E Isolated from Plasma Collected from a Haitian Child in 2016
Authors: Bonny Tania S. , Subramaniam Kuttichantran , Waltzek Thomas B. , Elbadry Maha A. , Beau De Rochars Valery Madsen , Telisma Taina , Rashid Mohammed , Morris J. Glenn , Lednicky John A. 
Published: November 2017

ABSTRACTHuman coronavirus strain 229E (HCoV-229E) and human alphaherpesvirus 1 were isolated from the plasma of a Haitian child in 2016 with suspected arbovirus diseases. To our knowledge, this is the first description of HCoV-229E in human plasma, which is the focus of this article.
Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002
T
Authors: Tsubouchi Taishi , Kaneko Yukihiro 
Published: November 2017

ABSTRACT

We report the 3.2-Mb draft genome sequence of
Brevundimonas denitrificans
strain TAR-002
T
, isolated from deep-sea floor sediment. The draft genome sequence of strain TAR-002
T
consists of 3,231,216 bp in 44 contigs, with a G+C content of 68.47%, 3,866 potential coding sequences (CDSs), 3 rRNAs, and 45 tRNAs.
Draft Genome Sequence of an Indian Marine Cyanobacterial Strain with Fast Growth and High Polyglucan Content
Authors: Pathania Ruchi , Ahmad Ahmad , Srivastava Shireesh 
Published: November 2017

ABSTRACT

Marine cyanobacteria play an important role in global carbon cycling and are a potential source of polyglucans for biotechnological purposes. This report provides the draft sequence of an Indian marine cyanobacterium,
Synechococcus elongatus
BDU 130192, which shows fast growth and high polyglucan content. The genome sequence will help in understanding the unique properties of this organism.
Complete Genome Sequences of Campylobacter jejuni Strains Isolated from Retail Chicken and Chicken Gizzards
Authors: Marasini Daya , Fakhr Mohamed K. 
Published: November 2017

ABSTRACT

Genome sequences of
Campylobacter jejuni
FJ3124 and ZP3204 isolated from retail chicken gizzards and
Campylobacter jejuni
TS1218 isolated from retail chicken showed the presence of 1,694,324-, 1,763,161-, and 1,762,596-bp circular chromosomes, respectively.
Campylobacter jejuni
ZP3204 and TS1218 harbored large tetracycline resistance plasmids with type IV secretion systems.
Maternal and neonatal outcomes of vaginal breech delivery for singleton term pregnancies in a carefully selected Cameroonian population: a cohort study
Authors: Dohbit Julius Sama , Foumane Pascal , Tochie Joel Noutakdie , Mamoudou Fadimatou , Temgoua Mazou N , Tankeu Ronni , Aletum Veronica , Mboudou Emile 
Published: November 2017

Background and objectivesVaginal breech delivery (VBD) is known to be associated with more perinatal and maternal complications. Very few studies on the subject have been carried out in poor-resource settings. The aim of this study was to determine maternal and neonatal outcomes in carefully selected cases of VBD for singleton term pregnancies in a tertiary centre in Cameroon.DesignA retrospective cohort study.SettingA tertiary hospital in Yaounde, Cameroon.ParticipantsCases of VBD of newborns weighing 2500–3500 g were matched in a ratio of 1:4 to consecutive vaginal cephalic deliveries (VCDs) of newborns weighing 2500–3500 g over a 5-year period. Both groups were matched for maternal age and parity. We excluded cases of multiple gestations, footling breech, clinically inadequate maternal pelvis, preterm delivery, post-term pregnancies, fetal demise prior to the onset of labour, placenta praevia and fetal anomaly incompatible with vaginal delivery.Outcome measuresNeonatal and maternal adverse outcomes of VBD observed till 6 weeks after delivery analysed using Bonferroni correction.ResultsFifty-three (53) VBDs were matched against 212 VCD. Unlike women who had VCD, those who underwent VBD were more likely to have prolonged labour (OR 8.05; 95% CI 3.00 to 11.47; P<0.001), and their newborns were more likely to suffer from birth asphyxia (OR 10.24; 95% CI 4.92 to 21.31; P<0.001).ConclusionThe study infers a strong association between VBD of singleton term pregnancies and maternofetal morbidity when specific protocols are applied. This, however, failed to translate into higher differences in perinatal mortality. This finding does not discount the role of VBD in low-income countries, but we emphasise the need for specific precautions like close monitoring of labour and adequate anticipation for neonatal resuscitation in order to reduce these complications.
Use of driving-impairing medicines by a Spanish population: a population-based registry study
Authors: Gutierrez-Abejón Eduardo , Herrera-Gómez Francisco , Criado-Espegel Paloma , Alvarez F Javier 
Published: November 2017

ObjectiveTo assess the use of driving-impairing medicines (DIM) in the general population with special reference to length of use and concomitant use.DesignPopulation-based registry study.SettingThe year 2015 granted medicines consumption data recorded in the Castile and León (Spain) medicine dispensation registry was consulted.ParticipantsMedicines and DIM consumers from a Spanish population (Castile and León: 2.4 million inhabitants).ExposureMedicines and DIM consumption. Patterns of use by age and gender based on the length of use (acute: 1–7 days, subacute: 8–29 days and chronic use: ≥30 days) were of interest. Estimations regarding the distribution of licensed drivers by age and gender were employed to determine the patterns of use of DIM.ResultsDIM were consumed by 34.4% (95% CI 34.3% to 34.5%) of the general population in 2015, more commonly with regularity (chronic use: 22.5% vs acute use: 5.3%) and more frequently by the elderly. On average, 2.3 DIM per person were dispensed, particularly to chronic users (2.8 DIM per person). Age and gender distribution differences were observed between the Castile and León medicine dispensation registry data and the drivers’ license census data. Of all DIM dispensed, 83.8% were in the Anatomical Therapeutic Chemical code group nervous system medicines (N), which were prescribed to 29.2% of the population.ConclusionsThe use of DIM was frequent in the general population. Chronic use was common, but acute and subacute use should also be considered. This finding highlights the need to make patients, health professionals, health providers, medicine regulatory agencies and policy-makers at large aware of the role DIM play in traffic safety.
Identifying clinical features in primary care electronic health record studies: methods for codelist development
Authors: Watson Jessica , Nicholson Brian D , Hamilton Willie , Price Sarah 
Published: November 2017

ObjectiveAnalysis of routinely collected electronic health record (EHR) data from primary care is reliant on the creation of codelists to define clinical features of interest. To improve scientific rigour, transparency and replicability, we describe and demonstrate a standardised reproducible methodology for clinical codelist development.DesignWe describe a three-stage process for developing clinical codelists. First, the clear definition a priori of the clinical feature of interest using reliable clinical resources. Second, development of a list of potential codes using statistical software to comprehensively search all available codes. Third, a modified Delphi process to reach consensus between primary care practitioners on the most relevant codes, including the generation of an ‘uncertainty’ variable to allow sensitivity analysis.SettingThese methods are illustrated by developing a codelist for shortness of breath in a primary care EHR sample, including modifiable syntax for commonly used statistical software.ParticipantsThe codelist was used to estimate the frequency of shortness of breath in a cohort of 28 216 patients aged over 18 years who received an incident diagnosis of lung cancer between 1 January 2000 and 30 November 2016 in the Clinical Practice Research Datalink (CPRD).ResultsOf 78 candidate codes, 29 were excluded as inappropriate. Complete agreement was reached for 44 (90%) of the remaining codes, with partial disagreement over 5 (10%). 13 091 episodes of shortness of breath were identified in the cohort of 28 216 patients. Sensitivity analysis demonstrates that codes with the greatest uncertainty tend to be rarely used in clinical practice.ConclusionsAlthough initially time consuming, using a rigorous and reproducible method for codelist generation ‘future-proofs’ findings and an auditable, modifiable syntax for codelist generation enables sharing and replication of EHR studies. Published codelists should be badged by quality and report the methods of codelist generation including: definitions and justifications associated with each codelist; the syntax or search method; the number of candidate codes identified; and the categorisation of codes after Delphi review.
13 Prophylactic antibiotics for penetrating injury: a review of practice at a major trauma centre, literature review and recommendations
Authors: Kamarova Marharyta , Kendall Richard 
Published: November 2017

BackgroundThere is a lack of clarity regarding the use of prophylactic antibiotics for patients presenting with penetrating injuries. A structured literature review and review of penetrating injury records in an MTC was undertaken with a view to help guide clinical practice.MethodSearches were conducted on Medline (1946–2017), Embase (1974–2017), and Cochrane (up to 2017) using key words pertaining to penetrating trauma, prophylactic antibiotics and infection. Cases of penetrating injury presenting to one MTC during 2015–2016 were extracted from the TARN database. Patient information (age, sex), injury details (ISS score, anatomical site, nature), antibiotic use in ED, and infectious outcomes were analysed.ResultsA 2012 systematic review by Bosmanet al.included 11 RCTs, totalling 1234 patients with blunt and penetrating chest injuries requiring tube thoracostomy. Those that were given prophylactic antibiotics were less likely to develop empyema (OR:0.32), pneumonia (OR:0.51) and wound infections (OR:0.41) compared to placebo.A 2013 Cochrane meta-analysis on penetrating abdominal trauma found no RCTs comparing infection outcomes for prophylactic antibiotics vs placebo. No further trials have since been done. EAST guidelines (2012) recommend a single dose of prophylactic antibiotics for penetrating abdominal trauma. No relevant trials were found for penetrating soft tissue injuries.70 penetrating injuries for 2015–2016 were recorded on TARN, 40 of which were transfers from other hospitals. Half of the total injuries were stabbings, with the rest being shootings, falls and crush injuries. 62.5% of patients were given prophylactic antibiotics in ED. 83% of the remaining patients received antibiotics for another indication.ConclusionsStrong evidence exists for the use of prophylactic antibiotics for chest wounds requiring tube thoracostomy. The Cochrane review concluded that there is no evidence base for prophylactic antibiotic use for penetrating abdominal trauma, with EAST recommendations based on weaker evidence.Drawing conclusions about infectious outcomes from TARN data is difficult due to low total numbers, differences in record-keeping for secondary transfers and a high proportion of patients with another requirement for antibiotics.For penetrating thoracic injury requiring chest drain there is evidence of benefit for prophylactic antibiotics, in other patients with penetrating injury due to the current lack of evidence, clinical judgement based on the circumstances of penetrating injury is recommended.
2 Major incident triage and the implementation of a new triage tool, the MPTT-24
Authors: Vassallo James , Smith Jason 
Published: November 2017

IntroductionOver the last decade, a number of European cities including London, have witnessed high profile terrorist attacks resulting in major incidents with large numbers of casualties. Triage, the process of categorising casualties on the basis of their clinical acuity, is a key principle in the effective management of major incidents.The Modified Physiological Triage Tool (MPTT) is a recently developed primary triage tool which in comparison to existing triage tools, including the 2013 UK NARU Sieve, demonstrates the greatest sensitivity at predicting need for life-saving intervention (LSI) within both military and civilian populations.To improve the applicability and usability of the MPTT we increased the upper respiratory rate threshold to 24 breaths per minute (MPTT-24), to make it divisible by four, and included an assessment of external catastrophic haemorrhage. The aim of this study was to conduct a feasibility analysis of the proposed MPTT-24 (figure 1).Figure 1MPTT-24MethodsA retrospective review of the Joint Theatre Trauma Registry (JTTR) and Trauma Audit Research Network (TARN) databases was performed for all adult (>18 years) patients presenting between 2006–2013 (JTTR) and 2014 (TARN). Patients were defined as priority one (P1) if they had received one or more life-saving interventions.Using first recorded hospital physiology, patients were categorised as P1 or not-P1 by existing triage tools and both MPTT and MPTT-24. Performance characteristics were evaluated using sensitivity, specificity, under and over-triage with a McNemar test to determine statistical significance.ResultsBasic study characteristics are shown in Table 1. Both the MPTT and MPTT-24 outperformed all existing triage methods with a statistically significant (p<0.001) absolute reduction of between 25.5%–29.5% in under-triage when compared to existing UK civilian methods (NARU Sieve). In both populations the MPTT-24 demonstrated an absolute reduction in sensitivity with an increase in specificity when compared to the MPTT. A statistically significant difference was observed between the MPTT and MPTT-24 in the way they categorised TARN and JTTR cases as P1 (p<0.001).Table 1Study characteristicsTable 2Performance analysisConclusionExisting UK methods of primary major incident triage, including the NARU Sieve, are not fit for purpose, with unacceptably high rates of under-triage. When compared to the MPTT, the MPTT-24 allows for a more rapid triage assessment and continues to outperform existing triage tools at predicting need for life-saving intervention. Its use should be considered in civilian and military major incidents.
20 Risk factors for admission at three, urban emergency departments in england: a cross-sectional analysis of attendances over one month
Authors: Pope Ian , Ismail Sharif , McCoy David , Harris Tim 
Published: November 2017

ObjectiveTo investigate factors associated with unscheduled admission following presentation to Emergency Departments (EDs) at three hospitals in England.Design and settingCross-sectional analysis of attendance data for patients from three urban EDs in England: a large teaching hospital and major trauma centre (Site 1), and two district general hospitals (Sites 2 and 3). Variables included: patient age, gender, ethnicity, deprivation score, arrival date and time, arrival by ambulance or otherwise, a variety of ED workload measures, inpatient bed occupancy rates and admission outcome. Coding inconsistencies in routine ED data used for this study meant that diagnosis could not be included.Outcome measureThe primary outcome for the study was unscheduled admission.ParticipantsAll adults aged 16 and over attending the three inner London EDs in December 2013. Data on 19 734 unique patient attendances were gathered.ResultsOutcome data were available for 19 721 attendances (>99%), of whom 6263 (32%) were admitted to hospital. Site 1 was set as the baseline site for analysis of admission risk. Risk of admission was significantly greater at Sites 2 and 3 (AOR relative to Site 1 for Site 2 was 1.89, 95% CI:1.74 to 2.05, p<0.001), and for patients of black or black British ethnicity (1.29, 1.16–1.44, p<0.001). Deprivation was strongly associated with admission. Analysis of departmental and hospital-wide workload pressures gave conflicting results, but proximity to the ‘four-hour target’ (a rule that limits patient stays in EDs to four hours in the NHS in England) emerged as a strong driver for admission in this analysis (3.61, 3.30–3.95, p<0.001).ConclusionThis study found statistically significant variations in odds of admission between hospital sites when adjusting for various patient demographic and presentation factors, suggesting important variations in ED- and clinician-level behaviour relating to admission decisions. The four-hour target is a strong driver for emergency admission.
21 Daily dynamic discharge – a whole system solution to ED crowding
Authors: Kerr Jacques , Maitland Helen , Bell Claire , White Julie , Hunter Alan 
Published: November 2017

IntroductionED crowding is associated with increased mortality, poor staff and patient experience, an increased inpatient length of stay and poor compliance with the four-hour emergency access standard.1Where crowding is caused by exit block, the focus needs to be on whole system patient management, reducing the temporal mismatch between admissions and discharges since at times of peak demand hospitals may become gridlocked until patients are discharged.In an attempt to tackle exit block, the Scottish Government Unscheduled Care Team have implemented the Daily Dynamic Discharge (DDD) approach, which aims to increase the number of inpatient discharges by 12 pm, thus enabling more timeous flow through the ED.MethodsA series of meetings were held between the Unscheduled Care Team and the clinical and managerial staff of Dumfries and Galloway Royal Infirmary over a two-week period to train staff on implementing the elements of the Daily Dynamic Discharge approach. These included holding a daily whiteboard meeting with input from the multidisciplinary team, early determination of an Estimated Date of Discharge (EDD) for each patient, and conducting ‘golden hour’ ward rounds whereby the highest acuity patients were seen first followed by those who were expected to be discharged that day, thus increasing the number of discharges by 12 pm.ResultsOver a twelve-week period the average number of weekly discharges increased from 26.5 to 30.2, i.e., an average increase of 3.7 discharges per week. Average length of stay dropped from 6.8 days to 6.2 days, a saving of 0.6 days.The median discharge time was 32 min earlier once DDD had been implemented. Previously, a third (33%) of patients were discharged before 4 pm; after implementation, this rose to 44%.DiscussionEmergency Department activity, and particularly crowding, is the barometer for the rest of the hospital, and the only way to guarantee that patients who require admission, get into the right bed, and in a timely way, is to ensure that the downstream wards discharge sufficient numbers early in the day to accommodate admissions from the ED.The DDD approach has been shown to be effective in increasing the number of discharges by 12 pm, smoothing the admission/discharge profile, and is now being adopted in other hospitals throughout Scotland.ReferenceRichardson DB. Increase in patient mortality at 10 days associated with emergency department overcrowding. Med J Aust2006;184(5):213–216.
25 Organ donation in emergency departments: an analysis of best practice
Authors: Empson Katja , Beale Sarah , Kerr Jacques , Gardiner Dale 
Published: November 2017

IntroductionThe 2015 RCEM End of Life Care best practice guideline highlighted the need for organ and tissue donation to be a usual part of end of life care in the Emergency Department (ED). NICE guideline states that all deaths meeting defined clinical triggers in the ED (in practice – mechanical ventilation, plan to withdraw life sustaining treatment, death expected) should prompt timely referral to organ donation services. Any family discussion in the ED regarding organ donation should be held collaboratively with a specialist nurse for organ donation (SNOD). What is the evidence in UK EDs that this is always the case?MethodologyThe NHS Blood and Transplant Potential Donor Audit, carried out by specialist nurses in organ donation, audits every death aged 80 years and under in UK Emergency Departments and Intensive Care Units. Data from the Potential Donor Audit was analysed and compared across the 12 Regional NHSBT teams.ResultsAlmost all deceased donors in the UK are admitted to hospital via an Emergency Department (ED). The number of patients dying in UK EDs aged under 80 years of age and under (1 st April 2015 to 31 st March 2016) is variable across the country and not directly correlated with population. Patients dying in ED, who meet criteria for referral is equally variable across the UK (Range 1% Scotland – 3.9% Eastern).PDA data (1 April 2016 – 31 March 2017) reveals that 284 patients died in ED meeting referral criteria but only 47% were referred (Range 22%–65% across the 12 regions). Longer 4 year analysis (1 st April 2012 – 31 st March 2016) demonstrated that up to 16% of these patients are on the Organ Donor Register. Of the 125 families approached in the ED (1 April 2016 – 31 March 2017) only 67% involved a SNOD (Range 0%–100% across the 12 regions).DiscussionIn 2017, with the endorsement of RCEM, NHS Blood and Transplant publishedOrgan Donation and the Emergency Department: A Strategy for Implementation of Best Practice.The strategy promotes identification and referral of potential organ donors in the emergency department and collaborative approach of their families when withdrawal of treatment is planned in the Emergency Department. Most importantly it is emphasised that organ donation should be firmly established as a usual part of end of life care irrespective of the location of the patient.Figure 1Audited deaths in ED by organ donation region 1st april 2015 to 31st march 2016Figure 2Died in emergency department meeting PDA referral criteria 1st April 2016 to 31st March 2017Figure 3Families approaches regarding organ donation in the ED 1st April 2016 to 31st March 2017