bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sedimentary architecture and depositional controls of a Holocene wave‐dominated barrier‐island system
Authors: Fruergaard Mikkel , Johannessen Peter N. , Nielsen Lars H. , Nielsen Lars , Møller Ingelise , Andersen Thorbjørn J. , Piasecki Stefan , Pejrup Morten 
Published: September 2017

AbstractBarrier‐island system evolution is controlled by internal and external forcing mechanisms, and temporal changes in these mechanisms may be recorded in the sedimentary architecture. However, the precise role of individual forcing mechanisms is rarely well understood due to limited chronological control. This study investigates the relative role of forcing conditions, such as antecedent topography, sea‐level rise, sediment supply, storms and climate changes, on the evolution of a Holocene wave‐dominated barrier‐island system. This article presents temporal reconstruction of the depositional history of the barrier‐island system of Rømø in the Wadden Sea in unprecedented detail, based on ground‐penetrating radar profiles, sediment cores, high‐resolution dating and palynological investigations, and shows that ca 8000 years ago the barrier island formed on a Pleistocene topographic high. During the initial phase of barrier evolution, the long‐term sea‐level rise was relatively rapid (ca 9 mm year−1) and the barrier was narrow and frequently overwashed. Sediment supply kept pace with sea‐level rise, and the barrier‐island system mainly aggraded through the deposition of a ca 7 m thick stack of overwash fans. Aggradation continued for ca 1700 years until sea‐level rise had decreased to <2 mm year−1. In the last ca 6000 years, the barrier prograded 4 to 5 km through deposition of a 10 to 15 m thick beach and shoreface unit, despite a long‐term sea‐level rise of 1 to 2 mm year−1. The long‐term progradation was, however, interrupted by a transgression between 4000 years and 1700 years ago. These results demonstrate that the large‐scale morphology of the Danish Wadden Sea shoreline influences the longshore sediment transport flux and the millennial‐scale dispersal of sediment along the shoreline. On decadal to centennial timescales, major storms induced intense beach and shoreface erosion followed by rapid recovery and progradation which resulted in a highly punctuated beach and shoreface record. Major storms contributed towards a positive sediment budget, and the sustained surplus of sediment was, and still is, instrumental in maintaining the aggradational–progradational state of the barrier island.
A Modified Carbapenem Inactivation Method, CIMTris, for Carbapenemase Production in Acinetobacter and Pseudomonas Species
Authors: Uechi Kohei , Tada Tatsuya , Shimada Kayo , Kuwahara-Arai Kyoko , Arakaki Momoko , Tome Takaaki , Nakasone Isamu , Maeda Shiro , Kirikae Teruo , Fujita Jiro 
Published: September 2017

ABSTRACT

The carbapenem inactivation method (CIM) and modified CIM (mCIM) are simple and economical phenotypic screening methods for detecting carbapenemase production in Gram-negative bacteria. Although the mCIM has been recommended by the Clinical and Laboratory Standards Institute, both the CIM and mCIM have limitations. This study describes another modified CIM, called CIMTris, in which carbapenemase was extracted from bacteria with 0.5 M Tris-HCl (pH 7.6) buffer. The ability of the CIMTris to detect carbapenemase production was examined in
Acinetobacter
and
Pseudomonas
species. The CIMTris had an overall sensitivity of 97.6% and an overall specificity of 92.6%, whereas the mCIM had a sensitivity of 45.1% and a specificity of 100% for the isolates tested. These findings indicate that the CIMTris is useful for detecting carbapenemase production in
Acinetobacter
and
Pseudomonas
species.
Implementation of a Clinical Decision Support Tool for Stool Cultures and Parasitological Studies in Hospitalized Patients
Authors: Nikolic D. , Richter S. S. , Asamoto K. , Wyllie R. , Tuttle R. , Procop G. W. 
Published: September 2017

ABSTRACT

There is substantial evidence that stool culture and parasitological examinations are of minimal to no value after 3 days of hospitalization. We implemented and studied the impact of a clinical decision support tool (CDST) to decrease the number of unnecessary stool cultures (STCUL), ova/parasite (O&P) examinations, and
Giardia
/
Cryptosporidium
enzyme immunoassay screens (GC-EIA) performed for patients hospitalized >3 days. We studied the frequency of stool studies ordered before or on day 3 and after day 3 of hospitalization (i.e., categorical orders/total number of orders) before and after this intervention and denoted the numbers and types of microorganisms detected within those time frames. This intervention, which corresponded to a custom-programmed hard-stop alert tool in the Epic hospital information system, allowed providers to override the intervention by calling the laboratory, if testing was deemed medically necessary. Comparative statistics were employed to determine significance, and cost savings were estimated based on our internal costs. Before the intervention, 129/670 (19.25%) O&P examinations, 47/204 (23.04%) GC-EIA, and 249/1,229 (20.26%) STCUL were ordered after 3 days of hospitalization. After the intervention, 46/521 (8.83%) O&P examinations, 27/157 (17.20%) GC-EIA, and 106/1,028 (10.31%) STCUL were ordered after 3 days of hospitalization. The proportions of reductions in the number of tests performed after 3 days and the associated
P
values were 54.1% for O&P examinations (
P
< 0.0001), 22.58% for GC-EIA (
P
= 0.2807), and 49.1% for STCUL (
P
< 0.0001). This was estimated to have resulted in $8,108.84 of cost savings. The electronic CDST resulted in a substantial reduction in the number of evaluations of stool cultures and the number of parasitological examinations for patients hospitalized for more than 3 days and in a cost savings while retaining the ability of the clinician to obtain these tests if clinically indicated.
Transcriptome Analysis of the Spodoptera frugiperda AscovirusIn VivoProvides Insights into How Its Apoptosis Inhibitors and Caspase Promote Increased Synthesis of Viral Vesicles and Virion Progeny
Authors: Zaghloul Heba A. H. , Hice Robert , Arensburger Peter , Federici Brian A. 
Published: September 2017

ABSTRACTAscoviruses are double-stranded DNA (dsDNA) viruses that attack caterpillars and differ from all other viruses by inducing nuclear lysis followed by cleavage of host cells into numerous anucleate vesicles in which virus replication continues as these grow in the blood. Ascoviruses are also unusual in that most encode a caspase or caspase-like proteins. A robust cell line to study the novel molecular biology of ascovirus replicationin vitrois lacking. Therefore, we used strand-specific transcriptome sequencing (RNA-Seq) to study transcriptionin vivoin third instars ofSpodoptera frugiperdainfected with the type species,Spodoptera frugiperda ascovirus1a(SfAV-1a), sampling transcripts at different time points after infection. We targeted transcription of two types of SfAV-1a genes; first, 44 core genes that occur in several ascovirus species, and second, 26 genes predictedin silicoto have metabolic functions likely involved in synthesizing viral vesicle membranes. Gene cluster analysis showed differences in temporal expression of SfAV-1a genes, enabling their assignment to three temporal classes: early, late, and very late. Inhibitors of apoptosis (IAP-like proteins; ORF016, ORF025, and ORF074) were expressed early, whereas its caspase (ORF073) was expressed very late, which correlated with apoptotic events leading to viral vesicle formation. Expression analysis revealed that a Diedel gene homolog (ORF121), the only known “virokine,” was highly expressed, implying that this ascovirus protein helps evade innate host immunity. Lastly, single-nucleotide resolution of RNA-Seq data revealed 15 bicistronic and tricistronic messages along the genome, an unusual occurrence for large dsDNA viruses.IMPORTANCEUnlike all other DNA viruses, ascoviruses code for an executioner caspase, apparently involved in a novel cytopathology in which viral replication induces nuclear lysis followed by cell cleavage, yielding numerous large anucleate viral vesicles that continue to produce virions. Our transcriptome analysis of genome expressionin vivoby the Spodoptera frugiperda ascovirus shows that inhibitors of apoptosis are expressed first, enabling viral replication to proceed, after which the SfAV-1a caspase is synthesized, leading to viral vesicle synthesis and subsequent extensive production of progeny virions. Moreover, we detected numerous bicistronic and tricistronic mRNA messages in the ascovirus transcriptome, implying that ascoviruses use other noncanonical translational mechanisms, such as internal ribosome entry sites (IRESs). These results provide the first insights into the molecular biology of a unique coordinated gene expression pattern in which cell architecture is markedly modified, more than in any other known eukaryotic virus, to promote viral reproduction and transmission.
Novel Role for Interleukin-17 in Enhancing Type 1 Helper T Cell Immunity in the Female Genital Tract following Mucosal Herpes Simplex Virus 2 Vaccination
Authors: Bagri Puja , Anipindi Varun C. , Nguyen Philip V. , Vitali Danielle , Stämpfli Martin R. , Kaushic Charu 
Published: September 2017

ABSTRACTIt is well established that interferon gamma (IFN-γ) production by CD4+T cells is critical for antiviral immunity against herpes simplex virus 2 (HSV-2) genital infection. However, the role of interleukin-17A (IL-17A) production by CD4+T cells in HSV-2 antiviral immunity is yet to be elucidated. Here we demonstrate that IL-17A plays an important role in enhancing antiviral T helper type 1 (Th1) responses in the female genital tract (FGT) and is essential for effective protection conferred by HSV-2 vaccination. While IL-17A did not play a critical role during primary genital HSV-2 infection, seen by lack of differences in susceptibility between IL-17A-deficient (IL-17A−/−) and wild-type (WT) C57BL/6 mice, it was critical for mediating antiviral responses after challenge/reexposure. Compared to WT mice,IL-17A−/−mice (i) infected intravaginally and reexposed or (ii) vaccinated intranasally and challenged intravaginally demonstrated poor outcomes. Following intravaginal HSV-2 reexposure or challenge, vaccinatedIL-17A−/−mice had significantly higher mortality, greater disease severity, higher viral shedding, and higher levels of proinflammatory cytokines and chemokines in vaginal secretions. Furthermore,IL-17A−/−mice had impaired Th1 cell responses after challenge/reexposure, with significantly lower proportions of vaginal IFN-γ+CD4+T cells. The impaired Th1 cell responses inIL-17A−/−mice coincided with smaller populations of IFN-γ+CD4+tissue resident memory T (TRM) cells in the genital tract postimmunization. Taken together, these findings describe a novel role for IL-17A in regulating antiviral IFN-γ+Th1 cell immunity in the vaginal tract. This strategy could be exploited to enhance antiviral immunity following HSV-2 vaccination.IMPORTANCET helper type 1 (Th1) immunity, specifically interferon gamma (IFN-γ) production by CD4+T cells, is critical for protection against genital herpesvirus (HSV-2) infection, and enhancing this response can potentially help improve disease outcomes. Our study demonstrated that interleukin-17A (IL-17A) plays an essential role in enhancing antiviral Th1 responses in the female genital tract (FGT). We found that in the absence of IL-17A, preexposed and vaccinated mice showed poor disease outcomes and were unable to overcome HSV-2 reexposure/challenge. IL-17A-deficient mice (IL-17A−/−) had smaller populations of IFN-γ+CD4+tissue resident memory T (TRM) cells in the genital tract postimmunization than did wild-type (WT) mice, which coincided with attenuated Th1 responses postchallenge. This has important implications for developing effective vaccines against HSV-2, as we propose that strategies inducing IL-17A in the genital tract may promote more effective Th1 cell immunity and better overall protection.
NLRX1 Mediates MAVS Degradation To Attenuate the Hepatitis C Virus-Induced Innate Immune Response through PCBP2
Authors: Qin Yuwen , Xue Binbin , Liu Chunyan , Wang Xiaohong , Tian Renyun , Xie Qinya , Guo Mengmeng , Li Guangdi , Yang Darong , Zhu Haizhen 
Published: September 2017

ABSTRACT
Activation of innate immunity is essential for host cells to restrict the spread of invading viruses and other pathogens. However, attenuation or termination of signaling is also necessary for preventing immune-mediated tissue damage and spontaneous autoimmunity. Here, we identify nucleotide binding oligomerization domain (NOD)-like receptor X1 (NLRX1) as a negative regulator of the mitochondrial antiviral signaling protein (MAVS)-mediated signaling pathway during hepatitis C virus (HCV) infection. The depletion of NLRX1 enhances the HCV-triggered activation of interferon (IFN) signaling and causes the suppression of HCV propagation in hepatocytes. NLRX1, a HCV-inducible protein, interacts with MAVS and mediates the K48-linked polyubiquitination and subsequent degradation of MAVS via the proteasomal pathway. Moreover, poly(rC) binding protein 2 (PCBP2) interacts with NLRX1 to participate in the NLRX1-induced degradation of MAVS and the inhibition of antiviral responses during HCV infection. Mutagenic analyses further revealed that the NOD of NLRX1 is essential for NLRX1 to interact with PCBP2 and subsequently induce MAVS degradation. Our study unlocks a key mechanism of the fine-tuning of innate immunity by which NLRX1 restrains the retinoic acid-inducible gene I-like receptor (RLR)-MAVS signaling cascade by recruiting PCBP2 to MAVS for inducing MAVS degradation through the proteasomal pathway. NLRX1, a negative regulator of innate immunity, is a pivotal host factor for HCV to establish persistent infection.

IMPORTANCE
Innate immunity needs to be tightly regulated to maximize the antiviral response and minimize immune-mediated pathology, but the underlying mechanisms are poorly understood. In this study, we report that NLRX1 is a proviral host factor for HCV infection and functions as a negative regulator of the HCV-triggered innate immune response. NLRX1 recruits PCBP2 to MAVS and induces the K48-linked polyubiquitination and degradation of MAVS, leading to the negative regulation of the IFN signaling pathway and promoting HCV infection. Overall, this study provides intriguing insights into how innate immunity is regulated during viral infection.
PP12 New indicators for measuring patient survival following ambulance service care
Authors: Coster Joanne , Jacques Richard , Turner Janette , Crum Annabel , Nicholl Jon , Niroshan Siriwardena A 
Published: September 2017

BackgroundDeveloping better measures of quality and performance are key priorities for ambulance services. Using multi-stage, multi-stakeholder consensus studies, we developed eight new indicators of ambulance service quality and performance. We present here a new indicator to measure rates of survival to 7 days post incident in people with a serious emergency condition.MethodsWe linked six months patient level Computer-Aided Dispatch (CAD) and electronic Patient Report Form (ePRF) data from one ambulance service with Hospital Episode Statistics (HES A and E/admitted patient data), and national mortality (ONS) information We identified a cohort of people with one of 16 serious emergency conditions, defined as conditions ‘where death could potentially be prevented by a good emergency system’. We created age and condition adjusted models to calculate two survival measures. 1) Survival to hospital admission, within 7 days of the ambulance call; 2) For patients admitted to hospital, survival to 7 days from admission.Results11 264 patients met the inclusion criteria. 1) 10 647 survived to admission and 617 (5.5%) died pre-admission. Most pre-admission deaths were in older people (42%>80 years) and occurred within 1 day of the ambulance call (87.8%). People with ruptured aortic aneurysm and asphyxiation were more likely to die pre-admission than those with other conditions. 2) Of the 10 647 patients admitted to hospital, 94% survived. Survival rates decreased with age: 100% of children under 11 years compared whereas 84% of those aged over 90 years survived to 7 days. People with cardiac arrest, septic shock and ruptured aortic aneurysm were also more likely to die in hospital.ConclusionsThese two indicators relate to people with a serious emergency condition who survive. Further work is being done to develop predictive models that can be used to assess trends over time. For example, survival may improve through taking the right patients to the right specialist care.
PP16 Creating a linked dataset to explore patient outcomes after leaving ambulance care
Authors: Crum Annabel , Coster Joanne , Turner Janette , Siriwardena Niro 
Published: September 2017

BackgroundMost English ambulance services have implemented electronic patient report forms (ePRF), enabling electronic capture of patient information; previously all information was collected using paper forms. This development brings new opportunities, including linking ambulance data to patient information post ambulance discharge and improving ambulance quality measures. This research aims to create a linked ambulance service, A and E, inpatient and mortality dataset.MethodsEMAS supplied CAD operational and ePRF clinical data from the study period to the University of Sheffield, and patient identifiers (name, date of birth, address, NHS number) to NHS Digital. NHS Digital traced missing NHS numbers, retrieved patient-level HES A and E, HES inpatient, and ONS mortality data, and returned this data to the University of Sheffield. We created a linked ambulance service and subsequent care dataset by linking EMAS clinical information to data from NHS Digital. This allows us to identify subsequent recontacts, A and E attendances, admissions and deaths.ResultsOur sample comprised only calls recorded via ePRF plus Hear and Treat – excluding 38.90% of total calls. 80.06% of patients in our sample were successfully traced by NHS Digital; unsuccessful traces were due to missing or incomplete CAD/ePRF data. Only CAD identifiers were available for hear and treat patients, limiting tracing success. Non-traced patients could not be linked to HES/ONS data. Of the successfully traced patients, 94.61% were linked to at least one record in the HES or mortality data.ConclusionsWe successfully created a linked dataset for 154927 EMAS patients. This can be used to identify patient outcomes after leaving ambulance care and to develop and test new ways of monitoring ambulance service care quality and performance. Missing information was problematic for data linkage and may be more common among patients who were unable to provide personal details on scene e.g. sicker patients or those who died.
PP17 Reliability and validity of an ambulance patient reported experience measure (a-prem): pilot study
Authors: Siriwardena Aloysius Niroshan , Togher Fiona , Akanuwe Joseph , Spaight Anne 
Published: September 2017

BackgroundThere are no prehospital ambulance Patient Reported Experience Measures (A-PREMs) routinely used to support service comparisons and improvement. We developed an A-PREM, generating items through secondary analysis of ambulance patient interview data, and refining the instrument using expert assessment and cognitive interviews of service users. We aimed to pilot the A-PREM (48 experience and 12 attribute items) investigating user acceptability, reliability and construct validity.MethodsAmbulance users attended by a UK regional ambulance service within the previous six months, excluding those suffering cardiac arrest, were sent a self-administered A-PREM. Returned questionnaires were entered into Microsoft Excel and imported into SPSS v22 for analysis. Experience items were recoded to range from 0 (don’t know/can’t remember) to 3 (best recorded experience). Descriptive analysis for item frequencies and missing values, reliability analyses for potential scales and tests of correlation and association were conducted.ResultsIn all, 111 A-PREMs (22.2%) were returned. Missing data were highest for call-taking items. There was a significant association with a shorter wait for first response for four items measuring overall experience of call-taking (χ, p=0.05), ambulance staff (p<0.001), ambulance overall (p=0.001) and A and E (p=0.023). Four separate experience scales encompassing call taking (AmbCallScore, α=0.91), care at scene (AmbCareScore, α=0.90), care on leaving the patient (AmbLeaveScore, α=0.69), and care on transport (AmbTranScore α=0.71), showed satisfactory to high internal consistencies and distributions indicating generally positive experiences. AmbCallScore, AmbCareScore and AmbLeaveScore showed significantly higher scores (ANOVA) with shorter wait to first response. There were no significant differences for overall measures or scales by sex or age of participant, whether they were transported to hospital or not and whether it was their first experience of the ambulance service.ConclusionOur findings show that the A-PREM should be tested more widely for evidence of reliability, validity and sensitivity to different care and settings.
PP20 Using conversation analysis (ca) to explore 999-call recordings: what can micro-analysis of ‘talk’ reveal about help seeking for low-acuity conditions?
Authors: Booker Matthew , Barnes Rebecca , Heawood Alison , Purdy Sarah 
Published: September 2017

BackgroundAscertaining the appropriate clinical urgency of a 999 call is vital to ensure optimal resource utilisation. With numbers of calls to ambulances services for lower-acuity situations continuing the rise, it is necessary to accurately identify early that the helpneededis not always exactly the same as the helpasked for. Undertaking effective prioritisation can be further complicated when the patient is not the caller. This study seeks to explore how a detailed analysis of dialogue between call-taker and caller might better understand how talk is used to convey and respond to expectations and anxieties.MethodAudio recordings of 45 telephone calls made through the ‘999’ system to an NHS Ambulance Trust were transcribed according to Jeffersonian Notation, and analysed in accordance with the theory and conventions of Conversation Analysis (CA). CA is a well-established inductive method that focuses on extracting sequential patterns in high-quality recordings of interactional data. CA involves the search for communication actions and/or formats that form evidence of systematic usage that can be identified as a ‘practice’.ResultsAnalysis focussed on the opening sequence following the question “tell me exactly what happened”. Various phenomena contained within the subsequent dialogue are identified, including how the concept of ‘preference organisation’ can aid understanding of how certain triage dispositions might occur. Examples of how callers attempt to ‘repair’ talk, and offer ‘resistance’ to the perceived trajectory of the dialogue are also explored.ConclusionEven in very structured and partially-scripted interactions, revealing patterns of naturalistic utterances do occur. People use talk in 999 calls in distinct and definable ways to try and convey their expectations. Further focussed exploration of how people use the mechanics of talk in these situations is proposed, with the aim of identifying how cases might be managed differently through more nuanced triage questioning strategies.