bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping endangered areas for pest risk analysis.
Authors: Baker R. , Eyre D. , Brunel S. , Dupin M. , Reynaud P. , Jarošík V. 
Published: March 2015

Abstract

This chapter provides guidance on mapping risks posed by invasive alien species to support pest risk analysis (PRA), the process required to justify phytosanitary measures. Because pest risk mapping can be challenging and resource-intensive, the situations in which risk maps are particularly useful are highlighted. The procedures described focus on mapping areas where the pest can establish and potentially cause the greatest harm. In the first stage of risk mapping, the factors that might influence the potential distribution and impacts of an invasive alien species are identified and the data are assembled and mapped. In the second stage, the maps of each factor are combined using matrix rules to generate areas of potential establishment and highest risk. These general procedures are illustrated with two examples. Risk maps for the western corn rootworm, a maize pest that has invaded Europe, are based on the combination of maps of climatic suitability, the presence of sandy soils, the distribution of grain and forage maize and the value of these commodities in Europe. Uncertainty is estimated by varying the classification of climatic suitability to obtain the worst, best and most likely scenarios. Risk maps for the common water hyacinth, an invasive plant on the Iberian Peninsula, are based on maps of climatic suitability, the distribution of suitable wetland habitats and areas of conservation importance. The chapter concludes by summarizing some of the major challenges that remain to enhance the production of risk maps for PRA and their interpretation by risk managers.
Following the transportation trail to anticipate human-mediated invasions in terrestrial ecosystems.
Authors: Colunga-Garcia M. , Haack R. A. 
Published: March 2015

Abstract

Freight transportation is an important pathway for introduction and dissemination of invasive alien species. Identifying the final destination of imports is critical in determining the likelihood of introduction by invasive alien species. In this chapter, we used the Freight Analysis Framework (FAF) database to model freight transport of imports to the USA with urban areas as their final destination. We also used FAF-based projections for the year 2040 for 20 pathways consisting of four commodities from five world regions of origin. After modelling the final distribution of imports among urban areas in the USA, we characterized the distribution patterns of imports and assessed the introduction potential of invasive alien species to urban forests. Freight pattern analyses were conducted for one category of agricultural products and three categories of imports whose products or packaging materials are associated with invasive alien species: wood products, non-metallic mineral products and machinery. We found that the type of import and the world region of origin greatly influenced the final distribution of imported products. A simple pest risk assessment model for invasive alien species in urban forests was built based on the percentage of forestland and volume of imports for each urban area. We found that several urban areas are potentially highly vulnerable to introductions from invasive alien species, regardless of import pathway. We conclude that inclusion of freight movement information is critical for proper risk assessment of invasive alien species.
Simulation modelling of long-distance windborne dispersal for invasion ecology.
Authors: Parry H. R. , Eagles D. , Kriticos D. J. 
Published: March 2015

Abstract

We present a method to simulate atmospheric dispersal events in invasion ecology using examples of two economically important and highly mobile insect species: the bird cherry-oat aphid, Rhopalosiphum padi (which vectors yellow dwarf viruses to maize, barley, oats and wheat); and the biting midge, Culicoides imicola (which vectors bluetongue virus to a wide range of domestic and wild ruminants). We demonstrate this method using two available atmospheric trajectory modelling tools: HYSPLIT and PMTRAJ.
Predicting the economic impacts of invasive species: the eradication of the giant sensitive plant from Western Australia.
Authors: Cook D. C. , Sheppard A. , Liu Shuang Liu Shuang , Lonsdale W. M. 
Published: March 2015

Abstract

Economic analyses can facilitate biosecurity investment decisions in relation to pest risk management. The term biosecurity here refers to activities intended to prevent or control the introduction and spread of alien species that have a net negative effect on social welfare as determined by economic, environmental and social capital. The aim of the chapter is to demonstrate a model that indicates an appropriate level of funding that decision makers should allocate to specific pest management activities based on anticipated returns. We demonstrate the model with a recently introduced weed species to Western Australia, Mimosa pigra. This weed has been targeted for eradication and the analysis described here estimates the amount biosecurity managers should spend on eradication before costs begin to outweigh the likely returns.
Recognizing Potential Buprenorphine Medication Misuse: Product Packaging Does Not Degrade with Laundering
Authors: Gunderson Erik W. 
Published: March 2015

Background Expanded office-based buprenorphine opioid dependence treatment is associated with medication misuse and diversion consequences. Recurrent early refill requests may indicate misuse or diversion, although further research is needed on how to effectively recognize and address the issue in clinical practice. In the current study, patient report of damaged medication from laundering prompted evaluation of laundering on degradation of buprenorphine-containing product packages and contents. Methods Four buprenorphine product packaging approaches were assessed: 3 buprenorphine/naloxone placebo demonstration products (Suboxone and Bunavail film in foil wrappers and Zubsolv tablet in a blister pack) and Rexam-manufactured Screw-Loc closure pill container filled with a chewable aspirin as a surrogate for generic buprenorphine and buprenorphine/naloxone products. Two experimental laundering conditions, wash machine alone (W) and washer/dryer (W+D), were compared with unlaundered control (C) condition. Standard laundering settings were based on patient presentation. Products from the 2 experimental conditions and the control condition were labeled A, B, or C with counterbalanced assignment prior to visual examination of packaging and contents by the investigator who was blinded to condition. Results Packaging and contents remained intact for all products across experimental conditions, with only minor cosmetic effects compared with control. The W+D Suboxone film had 1–2 mm curling of the wrapper corners. Zubsolv blister packs had slight paper label fading (W+D > W). Bunavail W+D foil had an indentation outlining the inner film. The W+D bottle tablet had a ˜1 mm nick on one edge. No other differences were noted. After implementing more structured treatment and reviewing the results with the patient, he endorsed fabricating the laundering story to get additional medication. Conclusions Laundering is an unlikely cause of damaged buprenorphine-containing medication packaged in foil wrappers (Suboxone, Bunavail), blister pack (Zubsolv), or prescription pill bottle (generic buprenorphine or buprenorphine/naloxone products). Patient reports of such may indicate medication misuse or diversion.
RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis
Authors: Legendre Rachel , Baudin-Baillieu Agnès , Hatin Isabelle , Namy Olivier 
Published: March 2015

Abstract
Motivation: Ribosome profiling provides genome-wide information about translational regulation. However, there is currently no standard tool for the qualitative analysis of Ribo-seq data. We present here RiboTools, a Galaxy toolbox for the analysis of ribosome profiling (Ribo-seq) data. It can be used to detect translational ambiguities, stop codon readthrough events and codon occupancy. It provides a large number of plots for the visualisation of these events.
Availability and implementation: RiboTools is available from https://testtoolshed.g2.bx.psu.edu/view/rlegendre/ribo_tools as part of the Galaxy Project, under the GPLv3 licence. It is written in python2.7 and uses standard python libraries, such as matplotlib and numpy.
Contact: olivier.namy@igmors.u-psud.fr
Supplementary Information: Supplementary data are available from Bioinformatics online.
First Report of Tomato chlorotic spot virus in Hoya wayetii and Schlumbergera truncata
Authors: Baker Carlye A. , Adkins Scott 
Published: March 2015

To the best of our knowledge, this is the first report of TCSV infection of H. wayetii and S. truncata from any location, although other tospoviruses are known to infect these and related plant species. The identification of these two diverse plant species as the first reported natural ornamental hosts of TCSV has implications for TCSV epidemiology and management in ornamental and vegetable crops, which frequently share production space. Accepted by publication 15 January 2015. Published 25 February 2015.
Didymella bryoniae Isolates from Watermelon Seedlings in Florida Transplant Houses and Their Sensitivity to Boscalid
Authors: Hendricks Katherine E. , Roberts Pamela D. 
Published: March 2015

The purpose of this study was to examine why gummy stem blight was not being controlled in watermelon fields without a previous history of boscalid use and whether boscalid resistance could have originated from the transplants. The study evaluated Didymella bryoniae isolates collected from three Florida transplant houses for resistance to boscalid and compared the molecular mechanism of this resistance to that in the literature on isolates from North and South Carolina and Georgia. Accepted by publication 16 February 2015. Published 25 February 2015.
Rhizopus oryzae Associated with Melanagromyza splendida and Stem Disease of Sunflowers (Helianthus annuus) in California
Authors: Mathew Febina M. , Prasifka Jarrad R. , Gaimari Stephen D. , Shi Li , Markell Samuel G. , Gulya Thomas J. 
Published: March 2015

In September 2012, a female parental line in a Yolo Co., California, sunflower seed-production field began displaying external stem symptoms that could not be attributed to any known disease. Symptoms appeared to be associated with tunneling caused by an unidentified insect. Stems were collected, and Rhizopus oryzae (causal agent of Rhizopus head rot) and a minute fly, Melanagromyza splendida, were identified as the causal agent and associated insect, respectively. Further, R. oryzae was isolated from intact fly puparia. All commercial hybrids evaluated in the greenhouse were susceptible to stem infection by R. oryzae isolates. Yield implications and geographic distribution of this novel stem disease are unknown. This is the first report of R. oryzae causing stem disease in sunflowers, and of its association with M. splendida. Accepted for publication 10 January 2015. Published 25 March 2015.
Potential Role of Single Nucleotide Polymorphisms of XRCC1, XRCC3, and RAD51 in Predicting Acute Toxicity in Rectal Cancer Patients Treated With Preoperative Radiochemotherapy
Authors: Osti Mattia F. , Nicosia Luca , Agolli Linda , Gentile Giovanna , Falco Teresa , Bracci Stefano , Di Nardo Francesco , Minniti Giuseppe , De Sanctis Vitaliana , Valeriani Maurizio , Maglio Marianna , Borro Marina , Simmaco Maurizio , Enrici Riccardo M. 
Published: March 2015

Objectives:
To investigate the association between polymorphisms of DNA repair genes and xenobiotic with acute adverse effects in locally advanced rectal cancer patients treated with neoadjuvant radiochemotherapy.

Methods:
Sixty-seven patients were analyzed for the current study. Genotypes in DNA repair genes XRCC1 (G28152A), XRCC3 (A4541G), XRCC3 (C18067T), RAD51 (G315C), and GSTP1 (A313G) were determined by pyrosequencing technology.

Results:
The observed grade ≥3 acute toxicity rates were 23.8%. Chemotherapy and radiotherapy were interrupted for 46 and 14 days, respectively, due to critical complications. Four patients were hospitalized, 6 patients had been admitted to the ER, and 5 patients received invasive procedures (2 bladder catheters, 2 blood transfusions, and 1 growth factor therapy).

RAD51 correlated with acute severe gastrointestinal toxicity in heterozygosity (Aa) and homozygosity (AA) (P=0.036). Grade ≥3 abdominal/pelvis pain toxicity was higher in the Aa group (P=0.017) and in the Aa+AA group (P=0.027) compared with homozygous (aa) patients. Acute skin toxicity of any grade occurred in 55.6% of the mutated patients versus 22.8% in the wild-type group (P=0.04) for RAD51. XRCC1 correlated with skin toxicity of any grade in the Aa+AA group (P=0.03) and in the Aa group alone (P=0.044). Grade ≥3 urinary frequency/urgency was significantly higher in patients with AA (P=0.01), Aa (P=0.022), and Aa+AA (P=0.031) for XRCC3 compared with aa group.

Conclusions:
Our study suggested that RAD51, XRCC1, and XRCC3 polymorphisms may be predictive factors for radiation-induced acute toxicity in rectal cancer patients treated with preoperative combined therapy.
Long-term Outcomes after Off-Pump or Conventional Coronary Artery Bypass Grafting within a Veteran Population
Authors: Emerson Dominic A. , Hynes Conor F. , Trachiotis Gregory D. 
Published: March 2015

Objective Recently published data indicate that outcomes for off-pump coronary artery bypass grafting (OPCABG) may be inferior to conventional CABG (cCABG) within the Veteran population, but this has been only partly addressed within high-volume off-pump centers. Here, we seek to examine the long-term outcomes for these patients within the Veteran population at a single institution well experienced with OPCABG. Methods With the use of a preexisting in-house database, all patients who had undergone isolated CABG from 2000 to 2011 (n = 1125) were identified. From these data, 18 demographic and risk factors were compared and used to create a propensity score, which was used for matching between groups (OPCABG vs cCABG). The primary end point examined was death. Survival was analyzed using the Kaplan-Meier method and the log-rank test. Groups were compared using a Student t test or Fisher exact test, where appropriate. Results Unmatched OPCABG and cCABG groups were found to have significant differences in risk factors, with the OPCABG being a higher-risk population by ejection fraction, chronic obstructive pulmonary disease status, age, and renal function, among others (all P < 0.05). Kaplan-Meier analysis of the unmatched groups demonstrated an increased mortality rate within the higher-risk OPCABG group ( P = 0.0002). With the use of propensity score matching, 337 OPCABG patients were then matched to 337 cCABG controls. Comparison of demographic and risk factors between these matched groups did not demonstrate any statistically significant difference. When Kaplan-Meier analysis was performed for the matched groups, there was no statistically significant difference in survival. In addition, in the matched data set, OPCABG patients had a shorter average length of stay (8.2 vs 9.7 days, P = 0.022), shorter operative time (205 vs 270 minutes, P < 0.001), and lower rate of bleeding complications (0.9% vs 3.6%, P = 0.032). Conclusions In this high-volume off-pump center, matched OPCABG survival is similar to cCABG. Although recent data indicate that OPCABG survival may be worse than that of cCABG within the entire Veteran population, in centers well experienced with OPCABG, this does not seem to hold true. In addition, the benefit of decreased length of stay and lower morbidity rates seems to be significant. Further study of the long-term outcomes of OPCABG in high-volume Veteran's centers is warranted.
Prevalence, Natural History, and Outcome of Acute Fluid Collection and Pseudocyst in Children With Acute Pancreatitis
Authors: Bolia Rishi , Srivastava Anshu , Yachha Surender Kumar , Poddar Ujjal , Kumar Sheo 
Published: March 2015

ABSTRACTObjective:Recent years have witnessed an increase in acute pancreatitis (AP) in children; however, the natural history of acute fluid collection (AFC) and pseudocyst is largely unknown. We evaluated the frequency, clinical characteristics, and natural history of pseudocysts in children with AP.Methods:Children with AP admitted at Sanjay Gandhi Postgraduate Institute of Medical Sciences from 2001 to 2011 were enrolled and studied until complete resolution. Subjects with inadequate follow‐up, recurrent AP, and chronic pancreatitis were excluded.Results:Of the 58 children (43 boys, median age 14 [1–18] years) with AP, 34 (58.6%) and 22 (38%) developed AFC and pseudocyst, respectively. No difference in age (12 [4–18] vs 13 [1–16] years), etiology (idiopathic 64% vs 47% and traumatic 27.2% vs 22.2%), and systemic complications (pulmonary [18% vs 11%], renal [22.7% vs 11%], and shock [13.6% vs 10%]) was observed between children with and without pseudocyst. A total of 11 of the 22 subjects with pseudocyst underwent drainage, the commonest symptom requiring drainage being gastric outlet obstruction [n = 5] and infection [n = 2]. The 11 of the 22 children with AP and pseudocyst (size 6.4 [3–14.4] cm) showed spontaneous resolution (disappearance [n = 9] and significant reduction in size [n = 2]) during 110 (25–425) days. Symptomatic pseudocysts requiring drainage were more often secondary to traumatic AP (6/6 vs 2/14 [idiopathic], P = 0.0007) than asymptomatic pseudocysts resolving spontaneously. Overall, only 26.4% (9/34) children with AFC required drainage because of symptomatic pseudocyst.Conclusions:Among children with AP, 58.6% developed AFC and 38% developed pseudocysts. Only patients with symptomatic pseudocyst need drainage, and asymptomatic pseudocyst can be safely observed irrespective of size and duration of collection.
Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees
Authors: Solomon Brad , Kingsford Carleton 
Published: March 2015

AbstractEnormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequence Read Archive (SRA) are now available. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. A natural question is which of these experiments contain sequences that indicate the expression of a particular sequence such as a gene isoform, lncRNA, or uORF. However, at present this is a computationally demanding question at the scale of these databases.We introduce an indexing scheme, the Sequence Bloom Tree (SBT), to support sequence-based querying of terabase-scale collections of thousands of short-read sequencing experiments. We apply SBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues, comprising 5 terabytes of sequence. SBTs of this size can be queried for a 1000 nt sequence in 19 minutes using less than 300 MB of RAM, over 100 times faster than standard usage of SRA-BLAST and 119 times faster than STAR. SBTs allow for fast identification of experiments with expressed novel isoforms, even if these isoforms were unknown at the time the SBT was built. We also provide some theoretical guidance about appropriate parameter selection in SBT and propose a sampling-based scheme for potentially scaling SBT to even larger collections of files. While SBT can handle any set of reads, we demonstrate the effectiveness of SBT by searching a large collection of blood, brain, and breast RNA-seq files for all 214,293 known human transcripts to identify tissue-specific transcripts.The implementation used in the experiments below is in C++ and is available as open source athttp://www.cs.cmu.edu/∼ckingsf/software/bloomtree.
Burn or rot: leaf traits explain why flammability and decomposability are decoupled across species
Authors: Grootemaat Saskia , Wright Ian J. , van Bodegom Peter M. , Cornelissen Johannes H. C. , Cornwell William K. 
Published: March 2015

SummaryIn fireprone ecosystems, two important alternative fates for leaves are burning in a wildfire (when alive or as litter) or they get consumed (as litter) by decomposers. The influence of leaf traits on litter decomposition rate is reasonably well understood. In contrast, less is known about the influence of leaf traits on leaf and litter flammability. The aim of this study was twofold: (i) to determine which morphological and chemical leaf traits drive flammability and (ii) to determine whether different (combinations of) morphological and chemical leaf traits drive interspecific variation in decomposition and litter flammability and, in turn, help us understand the relationship between decomposability and flammability.To explore the relationships between leaf traits and flammability of individual leaves, we used 32 evergreen perennial plant species from eastern Australia in standardized experimental burns on three types of leaf material (i.e. fresh, dried and senesced). Next, we compared these trait–flammability relationships to trait–decomposability relationships as obtained from a previous decomposition experiment (focusing on senesced leaves only).Within the three parameters of leaf flammability that we measured, interspecific variation in time to ignition was mainly explained by specific leaf area and moisture content. Flame duration and smoulder duration were mostly explained by leaf dry mass and to a lesser degree by leaf chemistry, namely, nitrogen, phosphorus and tannin concentrations.The variation in the decomposition constant across species was unrelated to our measures of flammability. Moreover, different combinations of morphological and chemical leaf properties underpinned the interspecific variation in decomposability and flammability. In contrast to litter flammability, decomposability was driven by lignin and phosphorus concentrations.The decoupling of flammability and decomposability leads to three possible scenarios for species’ influence on litter fates: (i) fast‐decomposing species for which flammability is irrelevant because there will not be enough litter to support a fire; (ii) species with slow‐decomposing leaves and a high flammability; and (iii) species with slow‐decomposing leaves and a low flammability. We see potential for making use of the decoupled trait–decomposition–flammability relationships when modelling carbon and nutrient fluxes. Including information on leaf traits in models can improve the prediction of fire behaviour. We note that herbivory is another key fate for leaves, but this study was focused on fire and decomposition.