bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution
Authors: Haim Maria Sol , Mollerach Marta , Van Domselaar Gary , Teves Sergio A. , Degrossi José , Cardona Silvia T. 
Published: October 2016

ABSTRACT

Burkholderia contaminans
is a species of the
Burkholderia cepacia
complex, a group of bacteria that can grow in pharmaceutical products and are capable of infecting the immunocompromised and people with cystic fibrosis. Here, we report draft genome sequences for
Burkholderia contaminans
FFI-28, a strain isolated from a contaminated pharmaceutical solution.
Draft Genome Sequence of Elizabethkingia anophelis Strain EM361-97 Isolated from the Blood of a Cancer Patient
Authors: Lin Jiun-Nong , Yang Chih-Hui , Lai Chung-Hsu , Huang Yi-Han , Lin Hsi-Hsun 
Published: October 2016

ABSTRACT

Elizabethkingia anophelis
EM361-97 was isolated from the blood of a patient with nasopharyngeal carcinoma and lung cancer. We report the draft genome sequence of EM361-97, which contains a G+C content of 35.7% and 3,611 candidate protein-encoding genes.
Complete Genome Sequence of Aerococcus urinaeequi Strain AV208
Authors: Zhou Wanqing , Niu Dongmei , Zhang Zhifeng , Liu Yuan , Ning Mingzhe , Cao Xiaoli , Zhang Chunni , Shen Han 
Published: October 2016

ABSTRACT

Aerococcus urinaeequi
strain AV208 was isolated from an ascites sample from a patient with chronic kidney disease. The assembled genome contained 2,227,638 bp with a 39.1% G+C content. The genome harbors a
Tn1546
transposon-like structure with a
vanA
gene causing vancomycin resistance phenotypes of strain AV208.
Exit block in emergency departments: a rapid evidence review
Authors: Mason Suzanne , Knowles Emma , Boyle Adrian 
Published: October 2016

BackgroundExit block (or access block) occurs when ‘patients in the ED requiring inpatient care are unable to gain access to appropriate hospital beds within a reasonable time frame’. Exit block is an increasing challenge for Emergency Departments (EDs) worldwide and has been recognised as a major factor in leading to departmental crowding. This paper aims to identify empirical evidence, highlighting causes, effects and strategies to limit exit block.MethodsA computerised literature search was conducted of English language empirical evidence published between 2008 and 2014 using a combination of terms relating to exit block in ED.Results233 references were identified following the computerised search. Of these, 32 empirical articles of varying scientific quality were identified as relevant and results were presented under a number of headings. The majority of studies presented data relating to the impact of exit block on departments, patients and staff. A smaller number of articles evaluated interventions designed to reduce exit block. Evidence suggests that exit block is more likely to occur in more densely populated areas and less likely to occur in paediatric settings. Bed occupancy appears to be associated with exit block. Evidence supporting the impact of initiatives pointed towards increasing workforce and inpatient bed resources within the hospital setting to reduce block.ConclusionsFurther evidence is needed, especially within the NHS setting to increase the understanding around factors that cause exit block, and interventions that are shown to relieve it without compromising patient outcomes.
Variables associated with administration of analgesia, nurse-initiated analgesia and early analgesia in the emergency department
Authors: Taylor David McD , Chen Jessie , Khan Munad , Lee Marina , Rajee Mani , Yeoh Michael , Richardson Joanna R , Ugoni Antony M 
Published: October 2016

ObjectiveTo determine the patient and clinical variables associated with administration of any analgesia, nurse-initiated analgesia (NIA, prescribed and administered by a nurse) and early analgesia (within 30 min of presentation).MethodsWe undertook a retrospective cohort study of patients who presented to a metropolitan ED in Melbourne, Australia, during July and August, 2013. The ED has an established NIA programme. Patients were included if they were aged 18 years or more and presented with a painful complaint. The study sample was randomly selected from a list of all eligible patients. Data were extracted electronically from the ED records and by explicit extraction from the medical record. Logistic regression models were constructed to assess associations with the three binary study end points.Results1289 patients were enrolled. Patients were less likely to receive any analgesia if they presented 08:00–15:59 hours (OR 0.67, 95% CI 0.46 to 0.98) or 16:00–24:00 hours (OR 0.55, 95% CI 0.37 to 0.80) were triage category 5 (OR 0.20, 95% CI 0.08 to 0.49) or required an interpreter (OR 0.34, 95% CI 0.14 to 0.86). Patients were less likely to receive NIA or early analgesia if they were aged 56 years or more (OR 0.70 and 0.63; OR 0.57 and 0.21, respectively) or if they had received ambulance analgesia (OR 0.59, 95% CI 0.36 to 0.95; OR 0.38, 95% CI 0.20 to 0.74, respectively).ConclusionsPatients who present during the daytime, have a triage category of 5 or require an interpreter are less likely to receive analgesia. Older patients and those who received ambulance analgesia are less likely to receive NIA or early analgesia.
Is there a ‘weekend effect’ in major trauma?
Authors: Metcalfe David , Perry Daniel C , Bouamra Omar , Salim Ali , Lecky Fiona E , Woodford Maralyn , Edwards Antoinette , Costa Matthew L 
Published: October 2016

BackgroundMany previous studies have shown that patients admitted to hospital at weekends have worse outcomes than those on other days. It has been proposed that parity of clinical services throughout the week could mitigate the ‘weekend effect’. This study aimed to determine whether or not a weekend effect is observed within an all-hours consultant-led major trauma service.MethodsWe undertook an observational cohort study using data submitted by all 22 major trauma centres (MTCs) in England to the Trauma Audit & Research Network. The inclusion criteria were all major trauma patients admitted for at least 3 days, admitted to a high-dependency area, or deceased following arrival at hospital. Patients with Injury Severity Score (ISS) >15 were also analysed separately. The outcome measures were length of stay, in-hospital mortality and Glasgow Outcome Score (GOS). Secondary transfer of patients between hospitals was also included as a process outcome.ResultsThere were 49 070 patients, 22 248 (45.3%) of which had an ISS >15. Within multivariable logistic regression models, odds of secondary transfer into an MTC were higher at night (adjusted OR 2.05, 95% CI 1.93 to 2.19) but not during the day at weekends (1.09, 0.99 to 1.19). Neither admission at night nor at the weekend was associated with increased length of stay, worse GOS or higher odds of in-hospital death. These findings remained stable when confining analyses to the most severely injured patients (ISS >15), excluding transferred patients, and using a single mid-week (Wednesday) baseline.ConclusionsAfter adjustment for known confounders the weekend effect is not detectable within a regionalised major trauma service.
An evidence-based treatment algorithm for colorectal polyp cancers: results from the Scottish Screen-detected Polyp Cancer Study (SSPoCS)
Authors: Richards CH , Ventham NT , Mansouri D , Wilson M , Ramsay G , Mackay CD , Parnaby CN , Smith D , On J , Speake D , McFarlane G , Neo YN , Aitken E , Forrest C , Knight K , McKay A , Nair H , Mulholland C , Robertson JH , Carey FA , Steele RJC 
Published: October 2016

ObjectivesColorectal polyp cancers present clinicians with a treatment dilemma. Decisions regarding whether to offer segmental resection or endoscopic surveillance are often taken without reference to good quality evidence. The aim of this study was to develop a treatment algorithm for patients with screen-detected polyp cancers.DesignThis national cohort study included all patients with a polyp cancer identified through the Scottish Bowel Screening Programme between 2000 and 2012. Multivariate regression analysis was used to assess the impact of clinical, endoscopic and pathological variables on the rate of adverse events (residual tumour in patients undergoing segmental resection or cancer-related death or disease recurrence in any patient). These data were used to develop a clinically relevant treatment algorithm.Results485 patients with polyp cancers were included. 186/485 (38%) underwent segmental resection and residual tumour was identified in 41/186 (22%). The only factor associated with an increased risk of residual tumour in the bowel wall was incomplete excision of the original polyp (OR 5.61, p=0.001), while only lymphovascular invasion was associated with an increased risk of lymph node metastases (OR 5.95, p=0.002). When patients undergoing segmental resection or endoscopic surveillance were considered together, the risk of adverse events was significantly higher in patients with incomplete excision (OR 10.23, p<0.001) or lymphovascular invasion (OR 2.65, p=0.023).ConclusionA policy of surveillance is adequate for the majority of patients with screen-detected colorectal polyp cancers. Consideration of segmental resection should be reserved for those with incomplete excision or evidence of lymphovascular invasion.
All-cause and cancer-specific mortality in GORD in a population-based cohort study (the HUNT study)
Authors: Ness-Jensen Eivind , Gottlieb-Vedi Eivind , Wahlin Karl , Lagergren Jesper 
Published: October 2016

ObjectiveGastro-oesophageal reflux is a public health concern which could have associated oesophageal complications, including adenocarcinoma, and possibly also head-and-neck and lung cancers. The aim of this study was to test the hypothesis that reflux increases all-cause and cancer-specific mortalities in an unselected cohort.DesignThe Nord-Trøndelag health study (HUNT), a Norwegian population-based cohort study, was used to identify individuals with and without reflux in 1995–1997 and 2006–2008, with follow-up until 2014. All-cause mortality and cancer-specific mortality were assessed from the Norwegian Cause of Death Registry and Cancer Registry. Multivariable Cox regression was used to calculate HRs with 95% CIs for mortality with adjustments for potential confounders.ResultsWe included 4758 participants with severe reflux symptoms and 51 381 participants without reflux symptoms, contributing 60 323 and 747 239 person-years at risk, respectively. Severe reflux was not associated with all-cause mortality, overall cancer-specific mortality or mortality in cancer of the head-and-neck or lung. However, for men with severe reflux a sixfold increase in oesophageal adenocarcinoma-specific mortality was found (HR 6.09, 95% CI 2.33 to 15.93) and the mortality rate was 0.27 per 1000 person-years. For women, the corresponding mortality was not significantly increased (HR 3.68, 95% CI 0.88 to 15.27) and the mortality rate was 0.05 per 1000 person-years.ConclusionsIndividuals with severe reflux symptoms do not seem to have increased all-cause mortality or overall cancer-specific mortality. Although the absolute risk is small, individuals with severe reflux symptoms have a clearly increased oesophageal adenocarcinoma-specific mortality.
Induction of IFN-λ3 as an additional effect of nucleotide, not nucleoside, analogues: a new potential target for HBV infection
Authors: Murata Kazumoto , Asano Mai , Matsumoto Akihiro , Sugiyama Masaya , Nishida Nao , Tanaka Eiji , Inoue Taisuke , Sakamoto Minoru , Enomoto Nobuyuki , Shirasaki Takayoshi , Honda Masao , Kaneko Shuichi , Gatanaga Hiroyuki , Oka Shinichi , Kawamura Yuki I , Dohi Taeko , Shuno Yasutaka , Yano Hideaki , Mizokami Masashi 
Published: October 2016

ObjectiveThe clinical significance of polymorphisms in the interleukin-28B gene encoding interferon (IFN)-λ3, which has antiviral effects, is known in chronic HCV but not in HBV infection. Thus, we measured IFN-λ3 levels in patients with HBV and investigated its clinical significance and association with nucleos(t)ide (NUC) analogue administration.DesignSerum IFN-λ3 level was measured in 254 patients with HBV with varying clinical conditions using our own high sensitivity method. The resulting values were compared with various clinical variables. In addition, cell lines originating from various organs were cultured with NUCs, and the production of IFN-λ3 was evaluated.ResultsHigher serum IFN-λ3 levels were detected in the patients treated with nucleotide analogues (adefovir or tenofovir) compared with those treated with nucleoside analogues (lamivudine or entecavir). There were no other differences in the clinical background between the two groups. A rise in the serum IFN-λ3 levels was observed during additional administration of the nucleotide analogues. In vitro experiments showed that the nucleotide analogues directly and dose-dependently induced IFN-λ3 production only in colon cancer cells. Furthermore, the supernatant from cultured adefovir-treated colon cancer cells significantly induced IFN-stimulated genes (ISGs) and inhibited hepatitis B surface antigen (HBsAg) production in hepatoma cells, as compared with the supernatant from entecavir-treated cells.ConclusionsWe discovered that the nucleotide analogues show an additional pharmacological effect by inducing IFN-λ3 production, which further induces ISGs and results in a reduction of HBsAg production. These findings provide novel insights for HBV treatment and suggest IFN-λ3 induction as a possible target.
Petroleum systems and results of exploration on the Atlantic margins of the UK, Faroes & Ireland: what have we learnt?
Authors: Scotchman Iain C. , Doré Anthony G. , Spencer Anthony M. 
Published: October 2016

Abstract

The exploratory drilling of 200 wildcat wells along the NE Atlantic margin has yielded 30 finds with total discovered resources of
c.
4.1×10
9
barrels of oil equivalent (BOE). Exploration has been highly concentrated in specific regions. Only 32 of 144 quadrants have been drilled, with only one prolific province discovered – the Faroe–Shetland Basin, where 23 finds have resources totalling
c.
3.7×10
9
BOE. Along the margin, the pattern of discoveries can best be assessed in terms of petroleum systems. The Faroe–Shetland finds belong to an Upper Jurassic petroleum system. On the east flank of the Rockall Basin, the Benbecula gas and the Dooish condensate/gas discoveries have proven the existence of a petroleum system of unknown source – probably Upper Jurassic. The Corrib gas field in the Slyne Basin is evidence of a Carboniferous petroleum system. The three finds in the northern Porcupine Basin are from Upper Jurassic source rocks; in the south, the Dunquin well (44/23-1) suggests the presence of a petroleum system there, but of unknown source. This pattern of petroleum systems can be explained by considering the distribution of Jurassic source rocks related to the break-up of Pangaea and marine inundations of the resulting basins. The prolific synrift marine Upper Jurassic source rock (of the Northern North Sea) was not developed throughout the pre-Atlantic Ocean break-up basin system west of Britain and Ireland. Instead, lacustrine–fluvio-deltaic–marginal marine shales of predominantly Late Jurassic age are the main source rocks and have generated oils throughout the region. The structural position, in particular relating to the subsequent Early Cretaceous hyperextension adjacent to the continental margin, is critical in determining where this Upper Jurassic petroleum system will be most effective.
Aviat: a Lower Pleistocene shallow gas hazard developed as a fuel gas supply for the Forties Field
Authors: Rose Phil , Byerley Grant , Vaughan Owen , Cater John , Rea Brice R. , Spagnolo Matteo , Archer Stuart 
Published: October 2016

Abstract
The search for a gas source near to Apache's Forties Field in the North Sea was motivated by the prediction of an ever-increasing fuel gas shortfall as the field oil rate declined. The Central North Sea is well known for a large number of shallow gas hazards in the Pleistocene section that have historically caused blowouts during exploration and development. These gas accumulations typically show up as small bright anomalies on seismic data. In 2009, a large gas anomaly was identified to the east of Forties, and the Aviat Field was discovered in 2010 when exploration well 22/7-5 was drilled.
The Aviat Field reservoir is interpreted to be a subaqueous glacial outwash fan, consisting of silt-grade, rock flour material, deposited in front of a grounded ice sheet in some 400 m of water. Aviat sits on an overcompacted silty mudstone that was deformed by this ice sheet – the Crenulate Marker. The distribution of this horizon implies that the Early Pleistocene ice sheet covered at least the northern half of the UK North Sea.

Although the Aviat reservoir is thin (2–9 m thick), the well tests, pressure profiles and geophysical response demonstrate that the reservoir is well connected, extensive (over 35 km
2
) with high deliverability (up to 18 MMscfd achieved). Aviat was sanctioned in 2014 for development as a fuel gas supply for the Forties Field, with first gas achieved in July 2016.
Evaluating evidence from the Torridonian Supergroup (Scotland, UK) for eukaryotic life on land in the Proterozoic
Authors: Brasier A. T. , Culwick T. , Battison L. , Callow R. H. T. , Brasier M. D. 
Published: October 2016

Abstract
The Stoer, Sleat and Torridon groups lie unconformably on Palaeoproterozoic Lewisian metamorphic rocks. They contain organic carbon microfossils claimed to be non-marine and to include eukaryotes. We consider the evidence for terrestrial interpretations from each formation of the Torridonian Supergroup. The range of sedimentary structures and the boron content of illite led us to the overall conclusion that, based on the currently available evidence, the Torridonian Supergroup was probably entirely non-marine. Evidence for terrestrial life in these rocks comes from microbially induced sedimentary structures, including wrinkle structures with reticulate and elephant skin fabrics. Organic remains and microscopic carbonaceous compressions mostly reported from phosphates in the grey shales of the Stoer, Aultbea and Applecross formations are dominated by sphaeromorph acritarchs. The Diabaig phosphatic lagerstätte includes three-dimensional preservation of eukaryotic and prokaryotic organisms, providing remarkable insights into non-marine life around 1 billion years ago.

Supplementary material:
Taxonomy of Torridon Group microfossils from thin sections of phosphatic material (adapted from Battison 2012) is available at
https://doi.org/10.6084/m9.figshare.c.3522753
Investigating the extremes of the continuum of paracrine functions in CD34−/CD31+ CACs across diverse populations
Authors: Landers-Ramos Rian Q. , Sapp Ryan M. , VandeWater Emily , Macko Jennifer , Robinson Shawn , Wang Yan , Chin Eva R. , Spangenburg Espen E. , Prior Steven J. , Hagberg James M. 
Published: October 2016

Paracrine function of circulating angiogenic cells (CACs) is thought to contribute to vascular maintenance. We previously identified S100A8 and S100A9 secreted from physically inactive individuals’ CD34–/CD31+ CACs as negative regulators of capillary-like network formation. The purpose of this study was to investigate further the extremes of the continuum of CAC paracrine actions using two distinctly different groups representing “healthy” and “impaired” CAC function. We aimed to determine how capillary-like network formation in human umbilical vein endothelial cells (HUVECs) is affected by S100A8 and S100A9 in concentrations secreted by CACs from different ends of the health spectrum. CD34–/CD31+ CACs were isolated and cultured from 10 impaired function individuals defined as older (50–89 yr), non-ST-elevation myocardial infarction patients and 10 healthy individuals defined as younger (18–35 yr), healthy individuals, and conditioned media (CM) was generated. CM from the impaired function group's CACs significantly diminished network formation compared with CM from the healthy group ( P < 0.05). We identified elevations in S100A8, S100A9, and S100A8/A9 in the CM from the impaired function group ( P < 0.05). Pretreatment of HUVECs with inhibitors to a known S100A8 and S100A9 receptor, Toll-like receptor 4 (TLR4), but not receptor for advanced glycation end products, improved HUVEC network formation ( P < 0.05) compared with CM alone in the impaired function conditions. Exposure of HUVECs to the TLR4 signaling inhibitor also blocked recombinant S100A8- and S100A9-mediated reductions in network formation. Collectively, the results suggest that the mechanisms behind impaired CAC CD34–/CD31+ CM-mediated reductions in capillary-like network formation involve secretion of S100A8 and S100A9 and binding of these proteins to TLR4 receptors on HUVECs. NEW & NOTEWORTHY S100A8 and S100A9 proteins in concentrations secreted by CD34–/CD31+ circulating angiogenic cells (CACs) with impaired function reduce endothelial cell capillary-like network formation. These effects appear to be mediated by Toll-like receptor 4 and are absent with S100A8 and S100A9 in concentrations secreted by healthy CD34–/CD31+ CACs.
Oxidative phosphorylation: unique regulatory mechanism and role in metabolic homeostasis
Authors: Wilson David F. 
Published: October 2016

Oxidative phosphorylation is the primary source of metabolic energy, in the form of ATP, in higher plants and animals, but its regulation in vivo is not well understood. A model has been developed for oxidative phosphorylation in vivo that predicts behavior patterns that are both distinctive and consistent with experimental measurements of metabolism in intact cells and tissues. A major regulatory parameter is the energy state ([ATP]/[ADP][Pi], where brackets denote concentration). Under physiological conditions, the [ATP] and [Pi] are ~100 times that of [ADP], and most of the change in energy state is through change in [ADP]. The rate of oxidative phosphorylation ( y-axis) increases slowly with increasing [ADP] until a threshold is reached and then increases very rapidly and linearly with further increase in [ADP]. The dependence on [ADP] can be characterized by a threshold [ADP] (T) and control strength (CS), the normalized slope above threshold (Δ y/(Δ x/T). For normoxic cells without creatine kinase, T is ~30 µM and CS is ~10 s−1. Myocytes and cells with larger ranges of rates of ATP utilization, however, have the same [ADP]- and [AMP]-dependent mechanisms regulating metabolism and gene expression. To compensate, these cells have creatine kinase, and hydrolysis/synthesis of creatine phosphate increases the change in [Pi] and thereby CS. Cells with creatine kinase have [ADP] and [AMP], which are similar to cells without creatine kinase, despite the large differences in metabolic rate.31P measurements in human muscles during work-to-rest and rest-to-work transitions are consistent with predictions of the model.NEW & NOTEWORTHY A model developed for oxidative phosphorylation in vivo is shown to predict behavior patterns that are both novel and consistent with experimental measurements of metabolism in working muscle and other cells. The dependence of the rate on ADP concentration shows a pronounced threshold with a steep, nearly linear increase above the threshold. The threshold determines the homeostatic set point, and the slope above threshold determines how much metabolism changes in response to varied energy demand.