bluuebunny/crossref_metadata_2025_split huggingface dataset:
Process-based pest risk mapping using Bayesian networks and GIS.
Authors: Klinken R. D. van , Murray J. V. , Smith C. 
Published: March 2015

Abstract

Predicting the potential distribution of invasive alien pests (i.e. habitat suitability modelling) and their potential spread from existing populations (i.e. habitat susceptibility modelling) is critical to guide management responses at local, regional and national scales. We use the management of Chilean needle grass (Nassella neesiana) invasion in a 260,791 km2 part of eastern Australia as an example to describe a process-based approach for making such predictions with publicly available soft ware (e.g. Netica and ESRI products). The approach is deductive, with causal relationships captured in a Bayesian network and represented spatially at fine resolution using a geographic information system (GIS). Pest risk responses to changing environments, such as land-use change, climate change or altered flood regimes, and to management interventions can be tested through scenario analysis. Predictive risk mapping of invasive aliens is often knowledge-constrained; therefore, our approach seeks to capture the best available knowledge from often disparate sources in a transparent and explicit manner. For Chilean needle grass, we elicited process understanding from experts through a participatory approach, integrated an existing bioclimatic model and obtained our own field data. Our model, thereby, represents a hypothesis of what determines the distribution, abundance and spread of Chilean needle grass in the modelled region. Specifically, the model forecasts the likelihood of the weed reaching a threshold density (e.g. in this case, >30% ground cover) as defined by the experts. This approach to likelihood estimation contrasts with the presence/absence predictions of most other models. Modelling was done at a sufficiently fine spatial resolution (i.e. 30 m) to capture relevant invasion dynamics. Finally, we illustrate how validation can be used to give end users confidence in model predictions and to identify important knowledge gaps and uncertainties. We demonstrate how the resulting pest risk maps for Chilean needle grass can guide management decisions.
Identifying and assessing critical uncertainty thresholds in a forest pest risk model.
Authors: Koch F. H. , Yemshanov D. 
Published: March 2015

Abstract

Pest risk maps can provide helpful decision support for invasive alien species management, but often fail to address adequately the uncertainty associated with their predicted risk values. This chapter explores how increased uncertainty in a risk model's numeric assumptions (i.e. its principal parameters) might affect the resulting risk map. We used a spatial stochastic model, integrating components for entry, establishment and spread, to estimate the risks of invasion and their variation across a two-dimensional gridded landscape for Sirex noctilio, a non-native woodwasp detected in eastern North America in 2004. Historically, S. noctilio has been a major pest of pine (Pinus spp.) plantations in the southern hemisphere. We present a sensitivity analysis of the mapped risk estimates to variation in six key model parameters: (i) the annual probabilities of new S. noctilio entries at US and Canadian ports; (ii) the S. noctilio population-carrying capacity at a given location; (iii) the maximum annual spread distance; (iv) the probability of local dispersal (i.e. at a distance of 1 km); (v) the susceptibility of the host resource; and (vi) the growth rate of the host trees. We used Monte Carlo simulation to sample values from symmetric uniform distributions defined by a series of nested variability bounds around each parameter's initial values (i.e.±5%, ..., ±50%). The results show that maximum annual spread distance, which governs long-distance dispersal, was the most sensitive of the tested parameters. At±15% uncertainty in this parameter, mapped risk values shifted notably. No other parameter had a major effect, even at wider bounds of variation. The methods presented in this chapter are generic and can be used to assess the impact of uncertainties on the stability of pest risk maps or to identify any geographic areas for which management decisions can be made confidently, regardless of uncertainty.
Cues, creaks, and decoys: using passive acoustic monitoring as a tool for studying sperm whale depredation
Authors: Thode Aaron , Mathias Delphine , Straley Janice , O'Connell Victoria , Behnken Linda , Falvey Dan , Wild Lauren , Calambokidis John , Schorr Gregory , Andrews Russell , Liddle Joseph , Lestenkof Phillip 
Published: March 2015

AbstractSince 2003, a collaborative effort (SEASWAP) between fishers, scientists, and managers has researched how Alaskan sperm whales locate demersal longline fishing activity and then depredate sablefish from gear. Sperm whales constantly produce relatively low-frequency biosonar signals whenever foraging; therefore, over the past decade, passive acoustic monitoring (PAM) has become a basic tool, used for both measuring depredation activity and accelerating field tests of potential depredation countermeasures. This paper reviews and summarizes past published PAM research on SEASWAP, and then provides a detailed example of how PAM methods are currently being used to test countermeasures. The review covers two major research thrusts: (i) identifying acoustic outputs of fishing vessels that provide long-distance “cues” that attract whales to fishing activity; and (ii) validating whether distinctive “creak” sounds can be used to quantify and measure depredation rates, using both bioacoustic tags and statistical comparisons between visual and acoustic depredation estimates during federal sablefish surveys. The latter part of the paper then provides an example of how PAM is being used to study a particular potential countermeasure: an “acoustic decoy” which transmits fishing vessel acoustic cues to attract animals away from true fishing activity. The results of an initial 2011 field trial are presented to show how PAM was used to design the decoy signals and monitor the efficacy of the deployment. The ability of PAM to detect both whale presence and depredation behaviour has reduced the need to deploy researchers or other specialists on fishing cruises. Instead, volunteer fishers can deploy “user-friendly” acoustic recorders on their gear, greatly facilitating the testing of various deterrents, and providing the industry and regulators a convenient and unobtrusive tool for monitoring both the scale and long-term spread of this behaviour across the Alaskan fishery.
Antimicrobial stewardship: the role of scientists?
Authors: Bowater Laura 
Published: March 2015

Abstract
We continue to be warned about the risk of antibiotic resistance. This campaign has targeted medicine and agriculture, asking these industries to pay attention to the risks of widespread resistance and to cut the use of antibiotics wherever possible. However, there has been little to no mention of the widespread use of antibiotics in the scientific research community. As scientists we use antibiotics and antibiotic resistance as fundamental tools for our research; almost all conventional plasmids use an antibiotic resistance gene as a selectable marker, offering us an easy method of screening. With molecular biology and genetics at the heart of many research disciplines, these tools are ubiquitous. Scientists have a responsibility to monitor and reduce our use of antibiotics. With the growth and fast advancement of synthetic biology, it is timely for us to consider other options and to teach the next generation of researchers by example how to truly value antibiotics by using them more responsibly.
Activity of ceftaroline and comparator agents tested against Staphylococcus aureus from patients with bloodstream infections in US medical centres (2009–13)
Authors: Sader Helio S. , Farrell David J. , Flamm Robert K. , Jones Ronald N. 
Published: March 2015

Abstract

Objectives
The objective of this study was to evaluate the in vitro antimicrobial activity of ceftaroline and comparator agents tested against Staphylococcus aureus isolates causing bloodstream infection (BSI).

Methods
A total of 4426 S. aureus isolates from patients with BSI were collected in 150 medical centres in the USA in 2009–13 and tested for susceptibility to ceftaroline and comparators by the CLSI broth microdilution method.

Results
Overall, 45.5% of isolates were MRSA. Ceftaroline (MIC50/90, 0.25/1 mg/L) was active against 97.9% of S. aureus isolates at ≤1 mg/L (highest MIC, 2 mg/L). Daptomycin (MIC50/90, 0.25/0.5 mg/L), linezolid (MIC50/90, 1/2 mg/L) and vancomycin (MIC50/90, 1/1 mg/L) were active against ≥99.8% of isolates at the respective susceptible breakpoints. Susceptibility rates for clindamycin (MIC50/90, ≤0.25/&gt;2 mg/L) and levofloxacin (MIC50/90, ≤0.5/&gt;4 mg/L) were 80.8% and 59.2%, respectively. Against MSSA, ceftaroline (MIC50/90, 0.25/0.25 mg/L; 100.0% susceptible) was 16-, 4–8- and 4-fold more active in vitro (based on MIC50/90) than ceftriaxone (MIC50/90, 4/4 mg/L), linezolid (MIC50/90, 1/2 mg/L) and vancomycin (MIC50/90, 1/1 mg/L), respectively, and slightly more potent than daptomycin (MIC50/90, 0.25/0.5 mg/L). When tested against MRSA, ceftaroline was active against 95.4% and 100.0% of isolates at ≤1 and ≤2 mg/L, respectively. Moreover, ceftaroline retained significant activity against S. aureus with reduced susceptibility to vancomycin, daptomycin, clindamycin, levofloxacin and trimethoprim/sulfamethoxazole.

Conclusions
Ceftaroline demonstrated potent in vitro activity when tested against a large collection of contemporary (2009–13) S. aureus isolates causing BSI in US hospitals.
A needs assessment of health information technology for improving care coordination in three leading patient-centered medical homes
Authors: Richardson Joshua E , Vest Joshua R , Green Cori M , Kern Lisa M , Kaushal Rainu ,   the HITEC Investigators
Published: March 2015

AbstractObjective We investigated ways that patient-centered medical homes (PCMHs) are currently using health information technology (IT) for care coordination and what types of health IT are needed to improve care coordination.Materials and Methods A multi-disciplinary team of researchers conducted semi-structured telephone interviews with 28 participants from 3 PCMHs in the United States. Participants included administrators and clinicians from PCMHs, electronic health record (EHR) and health information exchange (HIE) representatives, and policy makers.Results Participants identified multiple barriers to care coordination using current health IT tools. We identified five areas in which health IT can improve care coordination in PCMHs: 1) monitoring patient populations, 2) notifying clinicians and other staff when specific patients move across care settings, 3) collaborating around patients, 4) reporting activities, and 5) interoperability. To accomplish these tasks, many participants described using homegrown care coordination systems separate from EHRs.Discussion The participants in this study have resources, experience, and expertise with using health IT for care coordination, yet they still identified multiple areas for improvement. We hypothesize that focusing health IT development in the five areas we identified can enable more effective care coordination. Key findings from this work are that homegrown systems apart from EHRs are currently used to support care coordination and, also, that reporting tools are key components of care coordination.Conclusions New health IT that enables monitoring, notifying, collaborating, reporting, and interoperability would enhance care coordination within PCMHs beyond what current health IT enables.
Linking acknowledgement to action: closing the loop on non-urgent, clinically significant test results in the electronic health record
Authors: Dalal Anuj K , Pesterev Bailey M , Eibensteiner Katyuska , Newmark Lisa P , Samal Lipika , Rothschild Jeffrey M 
Published: March 2015

Abstract
Failure to follow-up nonurgent, clinically significant test results (CSTRs) is an ambulatory patient safety concern. Tools within electronic health records (EHRs) may facilitate test result acknowledgment, but their utility with regard to nonurgent CSTRs is unclear. We measured use of an acknowledgment tool by 146 primary care physicians (PCPs) at 13 network-affiliated practices that use the same EHR. We then surveyed PCPs to assess use of, satisfaction with, and desired enhancements to the acknowledgment tool. The rate of acknowledgment of non-urgent CSTRs by PCPs was 78%. Of 73 survey respondents, 72 reported taking one or more actions after reviewing a CSTR; fewer (40–75%) reported that using the acknowledgment tool was helpful for a specific purpose. Forty-six (64%) were satisfied with the tool. Both satisfied and nonsatisfied PCPs reported that enhancements linking acknowledgment to routine actions would be useful. EHR vendors should consider enhancements to acknowledgment functionality to ensure follow-up of nonurgent CSTRs.
Clinical information modeling processes for semantic interoperability of electronic health records: systematic review and inductive analysis
Authors: Moreno-Conde Alberto , Moner David , Cruz Wellington Dimas da , Santos Marcelo R , Maldonado José Alberto , Robles Montserrat , Kalra Dipak 
Published: March 2015

Abstract
Objective This systematic review aims to identify and compare the existing processes and methodologies that have been published in the literature for defining clinical information models (CIMs) that support the semantic interoperability of electronic health record (EHR) systems.
Material and Methods Following the preferred reporting items for systematic reviews and meta-analyses systematic review methodology, the authors reviewed published papers between 2000 and 2013 that covered that semantic interoperability of EHRs, found by searching the PubMed, IEEE Xplore, and ScienceDirect databases. Additionally, after selection of a final group of articles, an inductive content analysis was done to summarize the steps and methodologies followed in order to build CIMs described in those articles.
Results Three hundred and seventy-eight articles were screened and thirty six were selected for full review. The articles selected for full review were analyzed to extract relevant information for the analysis and characterized according to the steps the authors had followed for clinical information modeling.
Discussion Most of the reviewed papers lack a detailed description of the modeling methodologies used to create CIMs. A representative example is the lack of description related to the definition of terminology bindings and the publication of the generated models. However, this systematic review confirms that most clinical information modeling activities follow very similar steps for the definition of CIMs. Having a robust and shared methodology could improve their correctness, reliability, and quality.
Conclusion Independently of implementation technologies and standards, it is possible to find common patterns in methods for developing CIMs, suggesting the viability of defining a unified good practice methodology to be used by any clinical information modeler.
Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network
Authors: Frey Lewis J , Sward Katherine A , Newth Christopher JL , Khemani Robinder G , Cryer Martin E , Thelen Julie L , Enriquez Rene , Shaoyu Su , Pollack Murray M , Harrison Rick E , Meert Kathleen L , Berg Robert A , Wessel David L , Shanley Thomas P , Dalton Heidi , Carcillo Joseph , Jenkins Tammara L , Dean J Michael 
Published: March 2015

Abstract
Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality.
Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers.
Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation.
Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes.
Radiation shielding for diagnostic radiology
Authors: Martin Colin J. 
Published: March 2015

Abstract
Scattered radiation makes up the majority of the stray radiation field around an X-ray unit. The scatter is linked to the amount of radiation incident on the patient. It can be estimated from quantities used to assess patient dose such as the kerma-area product, and factors have been established linking this to levels of scattered radiation for radiography and fluoroscopy. In radiography shielding against primary radiation is also needed, but in other modalities this is negligible, as the beam is intercepted by the image receptor. In the same way scatter from CT can be quantified in terms of dose-length product, but because of higher radiation levels, exposure to tertiary scatter from ceilings needs to be considered. Transmission requirements are determined from comparisons between calculated radiation levels and agreed dose criteria, taking into account the occupancy of adjacent areas. Thicknesses of shielding material required can then be calculated from simple equations.
Nulliparous pregnant women's narratives of imminent childbirth before and after internet‐based cognitive behavioural therapy for severe fear of childbirth: a qualitative study
Authors: Nieminen K , Malmquist A , Wijma B , Ryding E‐L , Andersson G , Wijma K 
Published: March 2015

ObjectiveTo describe the expectations concerning imminent childbirth before and after 8 weeks of internet‐based cognitive behavioural therapy (ICBT) among nulliparous pregnant women with severe fear of childbirth.DesignQualitative study of nulliparous pregnant women's narratives before and after CBT.SettingThe first ICBT programme for treating severe fear of childbirth.SampleFifteen nulliparous pregnant Swedish women with severe fear of childbirth participating in an ICBT self‐help programme.MethodsSemi‐structured open‐ended questions over the internet before and after 8 weeks of ICBT. The data were analysed using thematic analysis.Main outcome measuresThe participants’ narratives pertaining to five different situations during labour and delivery before and after ICBT.ResultsAfter therapy, participants described a more realistic attitude towards imminent childbirth, more self‐confidence and more active coping strategies. They perceived their partners and the staff as more supportive. They were more aware of the approaching meeting with their baby when giving birth.ConclusionsFollowing the ICBT programme, participants changed their attitude towards imminent childbirth from negative to more positive. This was manifested in positive and more realistic expectations regarding themselves, their partner and the staff that would look after them.
A View of Oral Communication Activities in Food Science From the Perspective of a Communication Researcher
Authors: Ann Vrchota Denise 
Published: March 2015

AbstractFood science researchers have pronounced the Institute of Food Technologists Success Skills to be the most important competency mastered by graduates entering the work force. Much of the content and outcomes of the Success Skills pertains to oral communication skills of public speaking and interpersonal and group communication. This qualitative study reports the results of an examination of oral communication activities in the classes of 9 faculty in the food science program at Iowa State Univ. The findings revealed communication activities in the classes that support the Success Skills oral communication mandates; however, the food science faculty did not explicitly teach these skills. Faculty assumed the students would acquire proficiency in oral communication through participation in disciplinary activities that required them to practice the skills. A situated communication framework cautions communication researchers to honor the oral communication traditions in other disciplines. Still, the practice of preparing students to communicate in professional contexts without formal instruction raises 2 questions from the perspective of a communication researcher: first, are students aware of the communication skills they applied in classroom activities? Second, are students able to transfer communication skills to other classes and, more importantly to professional practice, when they graduate, as a result of this approach? The discussion suggests exercises that direct students’ attention to the specific skill sets inherent in the oral communication activities in the Success Skills while enabling faculty to maintain the communication traditions of food science as they prepare students for professional practice.
Pyrosequencing andde novoassembly ofAntarctic krill (Euphausia superba)transcriptome to study the adaptability of krill to climate‐induced environmental changes
Authors: Meyer B. , Martini P. , Biscontin A. , De Pittà C. , Romualdi C. , Teschke M. , Frickenhaus S. , Harms L. , Freier U. , Jarman S. , Kawaguchi S. 
Published: March 2015

AbstractTheAntarctic krill,Euphausia superba, has a key position in theSouthernOcean food web by serving as direct link between primary producers and apex predators. The south‐westAtlantic sector of theSouthernOcean, where the majority of the krill population is located, is experiencing one of the most profound environmental changes worldwide. Up to now, we have only cursory information about krill's genomic plasticity to cope with the ongoing environmental changes induced by anthropogenicCO2emission. The genome of krill is not yet available due to its large size (about 48Gbp). Here, we present two cDNAnormalized libraries from whole krill and krill heads sampled in different seasons that were combined with two data sets of krill transcriptome projects, already published, to produce the first knowledgebase krill ‘master’ transcriptome. The new library produced 25% moreE. superbatranscripts and now includes nearly all the enzymes involved in the primary oxidative metabolism (Glycolysis,Krebs cycle and oxidative phosphorylation) as well as all genes involved in glycogenesis, glycogen breakdown, gluconeogenesis, fatty acid synthesis and fatty acidsβ‐oxidation. With these features, the ‘master’ transcriptome provides the most complete picture of metabolic pathways inAntarctic krill and will provide a major resource for future physiological and molecular studies. This will be particularly valuable for characterizing the molecular networks that respond to stressors caused by the anthropogenicCO2emissions and krill's capacity to cope with the ongoing environmental changes in theAtlantic sector of theSouthernOcean.
Rare case of primary pleural lymphoma presenting with pleural effusion
Authors: Sun Mei‐ling , Shang Bin , Gao Jian‐hua , Jiang Shu‐juan 
Published: March 2015

AbstractPrimary pleural lymphoma is rare and has been described in association with human immunodeficiency virus (HIV) infection or pyothorax. We report a rare case of primary pleural lymphoma in a 73‐year‐old man who presented with chest pain and no history of HIV infection or pyothorax. Chest imaging showed pleural thickening and pleural effusion. Thoracoscopic pleural biopsy was performed. Histopathological and immunohistochemical examinations conformed to that of a diffuse large B‐cell lymphoma. Physicians should be aware of this rare location of primary lymphoma and implement thoracoscopy as soon as possible.